# \#bed **URL:** https://help.galaxyproject.org/tag/bed/28.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [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 --- ## [What is the meaning of Reference Gene Model in FPKM Tools in Galaxy?](https://help.galaxyproject.org/t/what-is-the-meaning-of-reference-gene-model-in-fpkm-tools-in-galaxy/13141)
**Author:** [@Dr.Lida](https://help.galaxyproject.org/u/Dr.Lida)\ **Replies:** 1\ **Last updated:** [August 6, 2024, 5:36pm UTC](https://help.galaxyproject.org/t/what-is-the-meaning-of-reference-gene-model-in-fpkm-tools-in-galaxy/13141 "2024-08-06T17:36:08Z")
Hi everyone, i have 3 question: in “FPKM Counts” Tools, (that give us FPKM for each Gene), there is one Parameter as: “Reference Gene Model in BED format”, what is the meaning of that? It means the annotation file (GT… --- ## [Question about the 'get flanks' tool](https://help.galaxyproject.org/t/question-about-the-get-flanks-tool/8533)
**Author:** [@DWJM](https://help.galaxyproject.org/u/DWJM)\ **Replies:** 4\ **Last updated:** [August 25, 2022, 10:39pm UTC](https://help.galaxyproject.org/t/question-about-the-get-flanks-tool/8533 "2022-08-25T22:39:39Z")
Hi all, I’m using Galaxy to get terminator regions for all genes in a genome and I’m using the ‘get flanks’ tool. Question: does get flanks define the 3’ end of the gene on the sense strand as the ‘Around end’ regardle… --- ## [How to interpret bedcov tools output?](https://help.galaxyproject.org/t/how-to-interpret-bedcov-tools-output/1304)
**Author:** [@raminta.batiuskaite](https://help.galaxyproject.org/u/raminta.batiuskaite)\ **Replies:** 4\ **Last updated:** [June 7, 2022, 2:35pm UTC](https://help.galaxyproject.org/t/how-to-interpret-bedcov-tools-output/1304 "2022-06-07T14:35:27Z")
Hello. I would like to ask there I can find some information how to interpret BedCov tool output, because there is just numbers in the first line (header) and I can’t understand which column shows me sequence coverage? T… --- ## [Q: Which steps should I follow to answer this question? A: Using the tool "Group" to summarize data](https://help.galaxyproject.org/t/q-which-steps-should-i-follow-to-answer-this-question-a-using-the-tool-group-to-summarize-data/5845)
**Author:** [@Shaimaa\_Gamal](https://help.galaxyproject.org/u/Shaimaa_Gamal)\ **Replies:** 1\ **Last updated:** [April 21, 2021, 9:19pm UTC](https://help.galaxyproject.org/t/q-which-steps-should-i-follow-to-answer-this-question-a-using-the-tool-group-to-summarize-data/5845 "2021-04-21T21:19:03Z")
Which steps should I follow to answer this question? --- ## [How to filter FreeBayes output (vcf) file to specific region (SNP) bed file in usegalaxy](https://help.galaxyproject.org/t/how-to-filter-freebayes-output-vcf-file-to-specific-region-snp-bed-file-in-usegalaxy/5325)
**Author:** [@agrieng3](https://help.galaxyproject.org/u/agrieng3)\ **Replies:** 1\ **Last updated:** [February 4, 2021, 4:00pm UTC](https://help.galaxyproject.org/t/how-to-filter-freebayes-output-vcf-file-to-specific-region-snp-bed-file-in-usegalaxy/5325 "2021-02-04T16:00:48Z")
How to filter FreeBayes output (vcf) file to specific region (SNP) bed file in usegalaxy? just want to look at some of the positions (SNP) in bed file. tx --- ## [Extract Genomic DNA Invalid Lines Error](https://help.galaxyproject.org/t/extract-genomic-dna-invalid-lines-error/5015)
**Author:** [@aroebuck](https://help.galaxyproject.org/u/aroebuck)\ **Replies:** 6\ **Last updated:** [January 22, 2021, 5:49pm UTC](https://help.galaxyproject.org/t/extract-genomic-dna-invalid-lines-error/5015 "2021-01-22T17:49:26Z")
I am trying to run Extract Genomic DNA on a bed file in which I have an ID, the start coordinate and the end coordinate. The sequences I am targeting represent products for potential primers (~180 of them total). The Co… --- ## [How to delete rows with the same number in the bed file in usegalaxy](https://help.galaxyproject.org/t/how-to-delete-rows-with-the-same-number-in-the-bed-file-in-usegalaxy/4986)
**Author:** [@agrieng3](https://help.galaxyproject.org/u/agrieng3)\ **Replies:** 2\ **Last updated:** [December 11, 2020, 1:17pm UTC](https://help.galaxyproject.org/t/how-to-delete-rows-with-the-same-number-in-the-bed-file-in-usegalaxy/4986 "2020-12-11T13:17:47Z")
How to delete rows with the same number in the bed file in usegalaxy (If the number of the second column is equal to the number of the third column, delete that row) which tool could be useful? input: chr1 10 20 chr1… --- ## [Extract Genomic DNA- Chromosome was not found for hg19](https://help.galaxyproject.org/t/extract-genomic-dna-chromosome-was-not-found-for-hg19/4792)
**Author:** [@Shira-Fisher](https://help.galaxyproject.org/u/Shira-Fisher)\ **Replies:** 2\ **Last updated:** [November 20, 2020, 8:43pm UTC](https://help.galaxyproject.org/t/extract-genomic-dna-chromosome-was-not-found-for-hg19/4792 "2020-11-20T20:43:14Z")
Hay, I am trying to extract the DNA sequence from a bed file that contains “Chromosome”, “Start”, “End” and “Score” but I am getting 0 bytes and a warning message that (17033 warnings, 1st is: Chromosome by name ‘chr1’… --- ## [Bedtools Closest Error](https://help.galaxyproject.org/t/bedtools-closest-error/4399)
**Author:** [@Ankit\_Naik](https://help.galaxyproject.org/u/Ankit_Naik)\ **Replies:** 1\ **Last updated:** [September 11, 2020, 7:09pm UTC](https://help.galaxyproject.org/t/bedtools-closest-error/4399 "2020-09-11T19:09:44Z")
Got this error while using bedtools closest function Error: Type checker found wrong number of fields while tokenizing data line. Perhaps you have extra TAB at the end of your line? Check with “cat -t” How to solve th… --- ## [Tools to get precise annotated genomic regions for bedgraph input data](https://help.galaxyproject.org/t/tools-to-get-precise-annotated-genomic-regions-for-bedgraph-input-data/1105)
**Author:** [@yaklich1904](https://help.galaxyproject.org/u/yaklich1904)\ **Replies:** 5\ **Last updated:** [February 6, 2020, 3:26pm UTC](https://help.galaxyproject.org/t/tools-to-get-precise-annotated-genomic-regions-for-bedgraph-input-data/1105 "2020-02-06T15:26:03Z")
Please help me to find tools to get precise annotated genomic regions such as inton, exon, 5’ or 3’ UTR, promoter for the mouse genome, I have bedGraph files with genomic coordinates and I would like to get based on the … --- ## [Extract Genomic DNA won't work](https://help.galaxyproject.org/t/extract-genomic-dna-wont-work/2625)
**Author:** [@Ilse](https://help.galaxyproject.org/u/Ilse)\ **Replies:** 3\ **Last updated:** [December 11, 2019, 8:03pm UTC](https://help.galaxyproject.org/t/extract-genomic-dna-wont-work/2625 "2019-12-11T20:03:33Z")
Hay, I am trying to extact genomic DNA out of a FASTA file and a flanked VCF file. I have a VCF file and a FASTA file and I want to exctact the SNP’s with 200 bp flanks. First I uploaded my Fasta (this one is TAB deli… --- ## [I need a tool that can extract bases before a certain position](https://help.galaxyproject.org/t/i-need-a-tool-that-can-extract-bases-before-a-certain-position/1790)
**Author:** [@mlim](https://help.galaxyproject.org/u/mlim)\ **Replies:** 12\ **Last updated:** [July 24, 2019, 7:23pm UTC](https://help.galaxyproject.org/t/i-need-a-tool-that-can-extract-bases-before-a-certain-position/1790 "2019-07-24T19:23:12Z")
Hi everyone, Does anyone know of a command/package/program (either within or outside of Galaxy) that can spit out a file telling me the ~15 or so bases leading up to a certain position in a mouse genome? More informati… --- ## [Error executing tool: formatting problem with BED dataset](https://help.galaxyproject.org/t/error-executing-tool-formatting-problem-with-bed-dataset/507)
**Author:** [@ap2em](https://help.galaxyproject.org/u/ap2em)\ **Replies:** 2\ **Last updated:** [January 30, 2019, 6:11pm UTC](https://help.galaxyproject.org/t/error-executing-tool-formatting-problem-with-bed-dataset/507 "2019-01-30T18:11:48Z")
I am currently trying to upload bed files in order to use the deepTools computeMatrix tool. The bed files appear to be loaded in correctly, but whenever I run the computeMatrix tool I get the below error. The server cou… --- ## [UniProt SignalP Predictions: How tobautomatically remove predicted signal equence from FASTA](https://help.galaxyproject.org/t/uniprot-signalp-predictions-how-tobautomatically-remove-predicted-signal-equence-from-fasta/83)
**Author:** [@elabb\_fau](https://help.galaxyproject.org/u/elabb_fau)\ **Replies:** 5\ **Last updated:** [December 17, 2018, 10:31am UTC](https://help.galaxyproject.org/t/uniprot-signalp-predictions-how-tobautomatically-remove-predicted-signal-equence-from-fasta/83 "2018-12-17T10:31:44Z")
dear community, I was wondering if someone knows how to download the fasta sequences of proteins without their predicted signal sequence. I get the protein data from the UniProt database. At the moment I’m removing the …