# Sort status of BAM files after RNA STAR **URL:** \ **Category:** Uncategorized\ **Tags:** transcriptomics, resources, tool-help, rna\_star\ **Created:** [May 17, 2023, 11:41am UTC](https://help.galaxyproject.org/t/sort-status-of-bam-files-after-rna-star/10076 "2023-05-17T11:41:40Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![agschindler](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@agschindler](https://help.galaxyproject.org/u/agschindler)\ **Post date:** [May 17, 2023, 11:41am UTC](https://help.galaxyproject.org/t/sort-status-of-bam-files-after-rna-star/10076/1 "2023-05-17T11:41:40Z")
Hi, I am new to Galaxy. Are the BAM files generated after mapping using RNA STAR (version 2.7.8a+galaxy1 or newer) sorted (either by coordinate or name or tag)? After clicking on the ‘i’ logo for the ‘\*.mapped.bam’ dataset details, the dataset information section says the format is BAM. The ‘Tool Standard Output’ is as follows: Apr 28 20:52:35 … started STAR run Apr 28 20:52:35 … starting to generate Genome files Apr 28 20:53:23 … processing annotations GTF Apr 28 20:53:54 … starting to sort Suffix Array. This may take a long time… Apr 28 20:54:14 … sorting Suffix Array chunks and saving them to disk… Apr 28 21:13:08 … loading chunks from disk, packing SA… Apr 28 21:14:38 … finished generating suffix array Apr 28 21:14:38 … generating Suffix Array index Apr 28 21:19:00 … completed Suffix Array index Apr 28 21:19:01 … inserting junctions into the genome indices Apr 28 21:21:04 … writing Genome to disk … Apr 28 21:21:07 … writing Suffix Array to disk … Apr 28 21:21:30 … writing SAindex to disk Apr 28 21:21:33 … finished successfully Apr 28 21:21:33 … started STAR run Apr 28 21:21:33 … loading genome Apr 28 21:21:55 … started mapping Apr 28 21:30:30 … finished mapping Apr 28 21:30:54 … started sorting BAM Apr 28 21:31:45 … finished successfully However, though this output is essentially the same for my ‘\*.transcriptome-mapped.bam’ file, its dataset information says the format is unsorted.bam. See attached screenshots. ![mappedbam](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/c77f533871688690619a24067dab41fb2b855481.png) ![transmappedbam](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/a/a10c2fc012342d3c65d6e747f738adbd9204180e.png) The 1st line of ‘_.mapped.bam’ file is ‘@HD VN:1.4 SO:coordinate’. So am I correct in assuming that perhaps it might be sorted by coordinate? The 1st line of '_.transcriptome-mapped.bam’ is not the same as the ‘\*.mapped.bam’ but rather is ‘@SQ SN:NR\_046018.2 LN:1652’. Do I still need to perform the Samtools sort operation for either one or both these files? I intend to use them as inputs for featureCounts. Thanks a lot for the help in advance. 🙂 ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [May 17, 2023, 5:43pm UTC](https://help.galaxyproject.org/t/sort-status-of-bam-files-after-rna-star/10076/2 "2023-05-17T17:43:10Z")
Hi @agschindler > [@agschindler](#): > > Do I still need to perform the Samtools sort operation for either one or both these files? I intend to use them as inputs for featureCounts. The **datatype** metadata describes the sort formats of bam data. 1. The first dataset with the **bam** datatype assigned is coordinate sorted. 2. The second dataset with the **unsorted.bam** datatype assigned is not. The first is what most people would be using with **Featurecounts**. Instead, for transcript level expression analysis, **Salmon** or **Kallisto** are probably “better” choices scientifically. But, you can of course try out different data/parameters with any and see what happens 🙂 to explore. Maybe you can figure out how to get the data you need in novel ways. > **[Transcriptomics / Tutorial List](https://training.galaxyproject.org/training-material/topics/transcriptomics/)** > > Training material for all kinds of transcriptomics analysis. ---
**Author:** ![agschindler](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@agschindler](https://help.galaxyproject.org/u/agschindler)\ **Post date:** [May 22, 2023, 5:37pm UTC](https://help.galaxyproject.org/t/sort-status-of-bam-files-after-rna-star/10076/3 "2023-05-22T17:37:40Z")
Hi @jennaj Thank you very much your reply. This is quite helpful. 🙂 ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 16, 2026, 5:59pm UTC](https://help.galaxyproject.org/t/sort-status-of-bam-files-after-rna-star/10076/4 "2026-04-16T17:59:23Z")