# \#text-manipulation **URL:** https://help.galaxyproject.org/tag/text-manipulation/29.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Extracting data from a .gff3 file](https://help.galaxyproject.org/t/extracting-data-from-a-gff3-file/17723)
**Author:** [@kate2](https://help.galaxyproject.org/u/kate2)\ **Replies:** 3\ **Last updated:** [May 18, 2026, 1:30pm UTC](https://help.galaxyproject.org/t/extracting-data-from-a-gff3-file/17723 "2026-05-18T13:30:45Z")
Afternoon, hopefully a simple question. I want to extract data from a .gff3 file and add it to the relevant gene id in a list of genes contained in a separate file, however the gene id in the .gff3 file is amongst other… --- ## [Unfold bug, missing newline char](https://help.galaxyproject.org/t/unfold-bug-missing-newline-char/17687)
**Author:** [@Alper\_Yilmaz](https://help.galaxyproject.org/u/Alper_Yilmaz)\ **Replies:** 3\ **Last updated:** [April 27, 2026, 7:36pm UTC](https://help.galaxyproject.org/t/unfold-bug-missing-newline-char/17687 "2026-04-27T19:36:37Z")
I’m having a problem with unfold tool. I uploaded this file to galaxy and used unfold. gene kegg gene1 map1,map2 gene2 - gene3 map1,map2,map3 I was expecting to have this format: gene1 map1 gene1 map2 … --- ## [Upload CRISPOR file in the right format (SMAP-design)](https://help.galaxyproject.org/t/upload-crispor-file-in-the-right-format-smap-design/17652)
**Author:** [@Ynske](https://help.galaxyproject.org/u/Ynske)\ **Replies:** 1\ **Last updated:** [April 13, 2026, 8:00pm UTC](https://help.galaxyproject.org/t/upload-crispor-file-in-the-right-format-smap-design/17652 "2026-04-13T20:00:55Z")
Hi, I’m using SMAP-design and want to use the pregenerated inputs (SMAP-selector) in combination with a CRIPSOR file input. I try to use Notepad++ (on a windows computer) and save the document as a .tsv file. When I upl… --- ## [Extract list of genes for annotated contig](https://help.galaxyproject.org/t/extract-list-of-genes-for-annotated-contig/838)
**Author:** [@andrej](https://help.galaxyproject.org/u/andrej)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:59am UTC](https://help.galaxyproject.org/t/extract-list-of-genes-for-annotated-contig/838 "2026-04-08T01:59:22Z")
Hi, I processed E. coli genome using standard pipeline (Unicycler) and annotated it using Prokka. Pasted below are first few lines from GFF file: ##gff-version 3 ##sequence-region 1 1 2860445 ##sequence-region 2 1 16… --- ## [Modifying text in a file](https://help.galaxyproject.org/t/modifying-text-in-a-file/4315)
**Author:** [@mich1213](https://help.galaxyproject.org/u/mich1213)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:08am UTC](https://help.galaxyproject.org/t/modifying-text-in-a-file/4315 "2026-04-08T01:08:30Z")
Hello, I am having some trouble with annotating my ID with Sailfish. I used Mouse gene mm10 (version 6) for my Sailfish. The error that I had with annotatemyID is same as below: Error in .testForValidKeys(x, keys, keyty… --- ## [ExomeDepth Column gene](https://help.galaxyproject.org/t/exomedepth-column-gene/10117)
**Author:** [@egarzon](https://help.galaxyproject.org/u/egarzon)\ **Replies:** 1\ **Last updated:** [May 24, 2023, 6:14pm UTC](https://help.galaxyproject.org/t/exomedepth-column-gene/10117 "2023-05-24T18:14:48Z")
Hello, I have tried to run ExomeDepth from galaxy but the generated output does not indicate column 2 of the gene and I am unable to graph the results, thanks for your help --- ## [Is it possible to add "add header" tool?](https://help.galaxyproject.org/t/is-it-possible-to-add-add-header-tool/16518)
**Author:** [@Achim\_Quaiser](https://help.galaxyproject.org/u/Achim_Quaiser)\ **Replies:** 4\ **Last updated:** [December 3, 2025, 10:29pm UTC](https://help.galaxyproject.org/t/is-it-possible-to-add-add-header-tool/16518 "2025-12-03T22:29:12Z")
Hello, I found the “add header” tool on the “usegalaxy.fr” but can’t find it on the “usegalaxy.eu”. Would it be possible to add please ? Here is the tool id toolshed.g2.bx.psu.edu/repos/estrain/add\_column\_headers/add\_… --- ## [Visualize with Krona error? Use Krona Pie Chart instead!](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111)
**Author:** [@Barry](https://help.galaxyproject.org/u/Barry)\ **Replies:** 12\ **Last updated:** [August 6, 2025, 10:52pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111 "2025-08-06T22:52:42Z")
I am trying to plot a Krona chart from a Kraken2 report, but I keep getting the following error: /cvmfs/main.galaxyproject.org/shed\_tools/toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona\_text/b14f1444e464/krona\_text/… --- ## [Tsv file upload fail for maaslin2](https://help.galaxyproject.org/t/tsv-file-upload-fail-for-maaslin2/15647)
**Author:** [@june](https://help.galaxyproject.org/u/june)\ **Replies:** 1\ **Last updated:** [August 5, 2025, 10:36pm UTC](https://help.galaxyproject.org/t/tsv-file-upload-fail-for-maaslin2/15647 "2025-08-05T22:36:06Z")
hi all :slight\_smile: Im trying to follow the Maaslin2 tutorial, on the Galaxy webtool, but I keep getting this error when I try to upload my abundance data file my file is in tsv format, and I cannot for the life of… --- ## [CSV output displays header twice](https://help.galaxyproject.org/t/csv-output-displays-header-twice/15588)
**Author:** [@Paul\_Wolfe](https://help.galaxyproject.org/u/Paul_Wolfe)\ **Replies:** 3\ **Last updated:** [May 30, 2025, 6:04pm UTC](https://help.galaxyproject.org/t/csv-output-displays-header-twice/15588 "2025-05-30T18:04:12Z")
Hello, I have been working on a new tool (reactome\_cli) but have run into what I think is a bug in the CSV display. See the attached image, the header is displayed twice. The CSV itself does not have the header line d… --- ## [Is there a way to combine paired-end and single-read RNASeq for a genome annotation?](https://help.galaxyproject.org/t/is-there-a-way-to-combine-paired-end-and-single-read-rnaseq-for-a-genome-annotation/15385)
**Author:** [@elpren](https://help.galaxyproject.org/u/elpren)\ **Replies:** 5\ **Last updated:** [May 19, 2025, 9:46pm UTC](https://help.galaxyproject.org/t/is-there-a-way-to-combine-paired-end-and-single-read-rnaseq-for-a-genome-annotation/15385 "2025-05-19T21:46:02Z")
Hi! I’m using published data and have no way of generating new RNA-Seq data. There are two different sets of RNA-Seq data published for my non-model organism, one is paired-end reads and one is single-reads. I’m using H… --- ## [Extracting feature sequences with gene ID information](https://help.galaxyproject.org/t/extracting-feature-sequences-with-gene-id-information/15326)
**Author:** [@cgreig](https://help.galaxyproject.org/u/cgreig)\ **Replies:** 3\ **Last updated:** [May 1, 2025, 4:42pm UTC](https://help.galaxyproject.org/t/extracting-feature-sequences-with-gene-id-information/15326 "2025-05-01T16:42:13Z")
To extract 5’ UTR sequences from my genome I have been able to use the Extract Features tool to pull out the locations of the 5’UTRs from the published genomic gff3 file and use this to extract fasta sequences from the g… --- ## [can you perform summary stats on multiple columns at once?](https://help.galaxyproject.org/t/can-you-perform-summary-stats-on-multiple-columns-at-once/15180)
**Author:** [@Avrilla01](https://help.galaxyproject.org/u/Avrilla01)\ **Replies:** 1\ **Last updated:** [April 7, 2025, 4:09am UTC](https://help.galaxyproject.org/t/can-you-perform-summary-stats-on-multiple-columns-at-once/15180 "2025-04-07T04:09:03Z")
doing an online course right now. We are doing the basics. To create summary stats we are using the ‘Group’ function. For this, the user need to add a new operation to calculate the mean for each column. Very long proce… --- ## [Case-sensitive Select tool?](https://help.galaxyproject.org/t/case-sensitive-select-tool/14972)
**Author:** [@katherine-d21](https://help.galaxyproject.org/u/katherine-d21)\ **Replies:** 3\ **Last updated:** [March 13, 2025, 9:49pm UTC](https://help.galaxyproject.org/t/case-sensitive-select-tool/14972 "2025-03-13T21:49:53Z")
Hello! I’m using the Select tool (Galaxy Version 1.0.4; link: Galaxy), My question is about whether this tool is case-sensitive. In particular, I am filtering out contaminant and decoy peptides, so here is how I set th… --- ## [How to solve problems with data formats: GTN Data Manipulation Olympics tutorials!](https://help.galaxyproject.org/t/how-to-solve-problems-with-data-formats-gtn-data-manipulation-olympics-tutorials/14970)
**Author:** [@AnneBollschu1](https://help.galaxyproject.org/u/AnneBollschu1)\ **Replies:** 2\ **Last updated:** [March 13, 2025, 1:57pm UTC](https://help.galaxyproject.org/t/how-to-solve-problems-with-data-formats-gtn-data-manipulation-olympics-tutorials/14970 "2025-03-13T13:57:31Z")
Hey, I created a file with three replicates of RNA counts of a total fraction and a cytoplasmic fraction (so 2x 3 replicates). It is a tab-text file, uploaded as tabular. I used this as single count matrix file and wrot… --- ## [Protein domain and motif identification](https://help.galaxyproject.org/t/protein-domain-and-motif-identification/14939)
**Author:** [@P.A.P\_KUMARA](https://help.galaxyproject.org/u/P.A.P_KUMARA)\ **Replies:** 1\ **Last updated:** [March 7, 2025, 7:05pm UTC](https://help.galaxyproject.org/t/protein-domain-and-motif-identification/14939 "2025-03-07T19:05:14Z")
I already ran the interproscan tool and get the domain and functional annotation results on my protein query. How I separate the domains and protein families. what are the tools that can be used for that and How I visual… --- ## [protein sequence](https://help.galaxyproject.org/t/protein-sequence/14938)
**Author:** [@E.L.A.T\_LIYANAGE](https://help.galaxyproject.org/u/E.L.A.T_LIYANAGE)\ **Replies:** 1\ **Last updated:** [March 7, 2025, 6:58pm UTC](https://help.galaxyproject.org/t/protein-sequence/14938 "2025-03-07T18:58:41Z")
I already have eggnog mapper data on orthologs. How can i separate this ortholog groups and visualize ortholog data as readable data --- ## [Having issues with my file formats, can't find "Check Format" section](https://help.galaxyproject.org/t/having-issues-with-my-file-formats-cant-find-check-format-section/14688)
**Author:** [@Hugo\_HAMMERLIN](https://help.galaxyproject.org/u/Hugo_HAMMERLIN)\ **Replies:** 9\ **Last updated:** [February 12, 2025, 5:55pm UTC](https://help.galaxyproject.org/t/having-issues-with-my-file-formats-cant-find-check-format-section/14688 "2025-02-12T17:55:22Z")
Hello, I’m really new to this platform, and I tried using the univariate test on already processed data. The only problem is that when I run the tool, I’m having this error: Column names of the dataMatrix are not ident… --- ## [How to downsize my 4Go FASTQ file to an 1Go FASTQ file?](https://help.galaxyproject.org/t/how-to-downsize-my-4go-fastq-file-to-an-1go-fastq-file/14665)
**Author:** [@dhebinger](https://help.galaxyproject.org/u/dhebinger)\ **Replies:** 1\ **Last updated:** [February 5, 2025, 7:29pm UTC](https://help.galaxyproject.org/t/how-to-downsize-my-4go-fastq-file-to-an-1go-fastq-file/14665 "2025-02-05T19:29:43Z")
Hi Galaxy community, I’m new here and first of all I’m absolutely not into bioinformatics and coding, everything is quite new to me! I’m trying to upload my fastq files here to first see if my sequences are good enough … --- ## [How to create karyotype for the circos plot](https://help.galaxyproject.org/t/how-to-create-karyotype-for-the-circos-plot/14623)
**Author:** [@P.A.P\_KUMARA](https://help.galaxyproject.org/u/P.A.P_KUMARA)\ **Replies:** 1\ **Last updated:** [February 1, 2025, 12:30am UTC](https://help.galaxyproject.org/t/how-to-create-karyotype-for-the-circos-plot/14623 "2025-02-01T00:30:41Z")
How to create karyotype for the circos? Are there any tools to make karyotype file in galaxy.org? How I find chromosome length/position in whole genome and Is there any tool for this?? --- ## [How to get galaxy to call transcript types from gene symbols?](https://help.galaxyproject.org/t/how-to-get-galaxy-to-call-transcript-types-from-gene-symbols/14431)
**Author:** [@Verdani](https://help.galaxyproject.org/u/Verdani)\ **Replies:** 1\ **Last updated:** [January 15, 2025, 7:07pm UTC](https://help.galaxyproject.org/t/how-to-get-galaxy-to-call-transcript-types-from-gene-symbols/14431 "2025-01-15T19:07:36Z")
Hello! Trying to get galaxy to search existing databases for the transcript type for each gene symbol found in 15x csv files. Have tried annotatemyID but there’s no readout for that. Does anyone know of a plugin or appro… --- ## [Merge Kraken2 & Bowtie2 classified reads](https://help.galaxyproject.org/t/merge-kraken2-bowtie2-classified-reads/14231)
**Author:** [@Laura\_Peirson](https://help.galaxyproject.org/u/Laura_Peirson)\ **Replies:** 2\ **Last updated:** [December 23, 2024, 12:38am UTC](https://help.galaxyproject.org/t/merge-kraken2-bowtie2-classified-reads/14231 "2024-12-23T00:38:22Z")
Goal: To merge classified reads from Kraken2 output with aligned reads from Bowtie2 output. I first classified reads using the PlusPFP reference db with Kraken2 which produced 1) a collection of classified read pairs in… --- ## [Create a collection from a tabular file](https://help.galaxyproject.org/t/create-a-collection-from-a-tabular-file/13771)
**Author:** [@rmassei](https://help.galaxyproject.org/u/rmassei)\ **Replies:** 2\ **Last updated:** [October 28, 2024, 6:47pm UTC](https://help.galaxyproject.org/t/create-a-collection-from-a-tabular-file/13771 "2024-10-28T18:47:42Z")
Hi! As an input, I have a single tabular file with several column as given in this example: col1 col2 col3 1 red dog 2 red cat 3 blue cat 4 blue dog 5 green dog I would like to create a collection from this singl… --- ## [Filter data on any column using simple expressions](https://help.galaxyproject.org/t/filter-data-on-any-column-using-simple-expressions/633)
**Author:** [@salvatore\_d](https://help.galaxyproject.org/u/salvatore_d)\ **Replies:** 4\ **Last updated:** [May 14, 2021, 3:19am UTC](https://help.galaxyproject.org/t/filter-data-on-any-column-using-simple-expressions/633 "2021-05-14T03:19:42Z")
Hi all. i have uploaded a file in wich I have to select the last two columns. I tried with the tool “Filter data on any column using simple expressions”, but evidently I’m missing something, because I don’t get what I w… --- ## [Create a new column in a table with specific patterns](https://help.galaxyproject.org/t/create-a-new-column-in-a-table-with-specific-patterns/13194)
**Author:** [@rmassei](https://help.galaxyproject.org/u/rmassei)\ **Replies:** 2\ **Last updated:** [August 13, 2024, 10:32am UTC](https://help.galaxyproject.org/t/create-a-new-column-in-a-table-with-specific-patterns/13194 "2024-08-13T10:32:24Z")
Hi! I have a csv file having two columns with the following series of values: Column1 Column2 3,4,5 7,8,9 which sequence of tools can I use in Galaxy to create a new column merging the values of Column1 and 2 in t… --- ## [Not able to view coulmn headers for DESEQ2](https://help.galaxyproject.org/t/not-able-to-view-coulmn-headers-for-deseq2/12620)
**Author:** [@jananis](https://help.galaxyproject.org/u/jananis)\ **Replies:** 1\ **Last updated:** [June 6, 2024, 10:14pm UTC](https://help.galaxyproject.org/t/not-able-to-view-coulmn-headers-for-deseq2/12620 "2024-06-06T22:14:31Z")
Ran feature counts results in deseq 2 but the results file does not show column name such as p value and logfold change --- ## [Running custom tool](https://help.galaxyproject.org/t/running-custom-tool/12510)
**Author:** [@chrisbioinfo](https://help.galaxyproject.org/u/chrisbioinfo)\ **Replies:** 1\ **Last updated:** [May 15, 2024, 5:36pm UTC](https://help.galaxyproject.org/t/running-custom-tool/12510 "2024-05-15T17:36:20Z")
Just wondering if there is a way to run custom python scripts on galaxy. Id like to reformat a VCF file for another tool and I am developing a quick script in python to do so. Ideally it would have vcf file input to a ts… --- ## [plotDEXSeq no output](https://help.galaxyproject.org/t/plotdexseq-no-output/12358)
**Author:** [@VI\_Rodriguez](https://help.galaxyproject.org/u/VI_Rodriguez)\ **Replies:** 5\ **Last updated:** [May 1, 2024, 5:46pm UTC](https://help.galaxyproject.org/t/plotdexseq-no-output/12358 "2024-05-01T17:46:29Z")
I tried to run plotDEXSeq on my output rds file (after converting it to rdata, database is mm10) but the resulting pdf file is empty. I’ve based the gene identifier on the DEXSeq result file but the error code says: No r… --- ## [Filter tabular data columns by arbitrary list](https://help.galaxyproject.org/t/filter-tabular-data-columns-by-arbitrary-list/11872)
**Author:** [@swbioinf](https://help.galaxyproject.org/u/swbioinf)\ **Replies:** 4\ **Last updated:** [March 14, 2024, 1:54am UTC](https://help.galaxyproject.org/t/filter-tabular-data-columns-by-arbitrary-list/11872 "2024-03-14T01:54:10Z")
Hello, I’m trying to figure out the galaxy way of subsetting columns by an arbitray list of column names. E.g. given a tabular file with irregular column names like so: gene A B sampleC D geneA 1 2 2 2 geneB 0 0 0 4 H… --- ## [Empty results from differential expression analysis using a Trinity assembly](https://help.galaxyproject.org/t/empty-results-from-differential-expression-analysis-using-a-trinity-assembly/11536)
**Author:** [@Yuqiao\_Min](https://help.galaxyproject.org/u/Yuqiao_Min)\ **Replies:** 3\ **Last updated:** [January 24, 2024, 10:58pm UTC](https://help.galaxyproject.org/t/empty-results-from-differential-expression-analysis-using-a-trinity-assembly/11536 "2024-01-24T22:58:46Z")
Hello, I keep getting empty results from differetial expression analysis tool. I have input like this Describe Samples.tabular expression matrix like this Please help. Thank you! [Next page](https://help.galaxyproject.org/tag/text-manipulation/29.md?match_all_tags=true&page=1&tags%5B%5D=text-manipulation)