Filter SAM or BAM tool -- "Select regions" filtering term formatting

usegalaxy.org support
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#1

Hello,

The most strange thing happened. I aligned a sample of raw RNA-seq data with HISAT2 (default settings). Then I used the function [Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region] to cut a 20 kb region that I am interested in. I don’t have a lot of storage space. So far so good. But when I opened it in IGV, there were more than 20 kb, way more. I could see the entire chromosome. I checked two more chromosomes and they were empty.

This happened with only one sample but I have 9 from the same batch that are processing right now.

I have followed this protocol before and nothing like this happened. The only time when I could see more outside my region, it was solely because the ends of the exon were exceeding it. Which made sense.

Do you have any opinions about it?

BTW I checked and the region that I selected was the right one.

1 Like
#2

Isn’t this tool producing a second output with your query turned into json format? This looks like a great opportunity to use this dataset and share its contents here.

#3

No, it only produces a smaller BAM, unless I am missing something

#4

Please try modifying your regions term.

Currently is similar to:

chrX: 1-1,000

When should be written as a contiguous term, with no space after the :

chrX:1-1,000

or this (the inclusion of commas , is optional):

chrX:1-1000

With the extra space included, the filter is malformed, and effectively ending up with an applied filter based on only the chromosome name (the first “word” in the term).

Tool form option and help:

filter-bam-select-regions
filter-bam-select-regions.png1276×194 17.7 KB

2 Likes
#5

Glad that worked!

I think we could (maybe) make the usage better. Not just for this tool, but any filter tool that has end-user free text (or a text file “list”) for region filters. If interested, I made a catch-all ticket here https://github.com/galaxyproject/usegalaxy-playbook/issues/227. The change could touch many tools, so please consider it a nice-to-have-wish-list-item for now.

Upvote/comment on the ticket if you agree this would help. Same for others reading! We don’t know definitively how often this is a usage issue end-users encounter, with filter tools in general or this tool specifically. Feedback from Galaxy users helps to inform the choices we make about changes/upgrades.

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#6

Ah sorry, my mistake. I confused this with the similar https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1.
Glad you got a solution from @jennaj.

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#7

No prob. But nice tool. I didn’t know about it. I am going to keep it in mind. Looks really useful.

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