what is fastq manupulation script for exclude rRNA contanimation

what is the script for fastq manipulation, for extract rRNA with 12-19 and 23-50 length ?

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Please see this tutorial:

You can search for tutorials under the top “Help” menu with keywords and get a brief description like this:


You won’t be removing, but keeping the rRNA yet the tools used should give some clues about the best tools to use, et cetera.

ive saw that tutorial. but in fastq manupulation … the script was not correct. the {12,19}$… does not working

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Please send in a bug report from the error dataset and leave that dataset and the inputs undeleted. I suspect there is a query formatting problem and can help you.

Important: Include a link to this post (URL) in the bug reporting comments so we can link the two, find your bug report, and prioritize it.

Issue resolved. Input datatype corrected and regular expression format corrected to match tutorial.

thank you for your kind support

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unfortunately i think there is some problem in that tutorial , if you look at my SRNA tutorial you can see the problem . the result of hisat2 in " Hierarchical read alignment to remove rRNA/miRNA reads" Step, is 0 byte. and cant use that as data. im using the own tutorial data to prove my data isnt the problem./

I’ll take a look on Monday.

Please send in a new bug report from the new errors - the one with your input data (rerun with prior fixes applied) and one using the tutorial data. It is fine is these are in different histories. Just include the post link again in the comments for all, so we can match everything up for overall context.

This tutorial is very new, we are in the middle of an upgrade cycle to Galaxy itself, and more problems are definitely possible. I’ll review.

it doesnt turn Red, So i cant report it as bug. the result in Hisat2 has o byte ,so its useless. i put it there untouched for yout, in my SRNA tutorial

Generate a share link to the histories and send those in to galaxy-bugs@lists.galaxyproject.org. Or, just reply to our prior Q&A on that mailing list.

Be sure to include this post link again and note which history was run with your data and which with the tutorial data, and the dataset numbers with the problems for each. Make sure to not delete the inputs or problematic job runs.

i did report that problem . but still no answer. when i Convert Bam to FAstq, it reduce the content of the Data and turn it to (0 byte).
its very annoying

@amir Thanks, I was waiting for you to let me know if/when you sent that in. I’ll review early next week (probably Monday).