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merenlab / illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
GNU General Public License v2.0
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using iu-remove-ids-from-fastq to remove read ids obtained from a bam file #19

Closed ShaiberAlon closed 5 years ago

ShaiberAlon commented 5 years ago

First of all, I wanted to say that this is a great tool, so I just wanted to thank the developers!

I am trying to use iu-remove-ids-from-fastq to remove some reads that were mapped using bowtie2, but I have the following problem: in the bam output from the bowtie2 mapping the reads look like this: fasta_02:23:B02CBACXX:8:2315:2667:7273

Whereas, if I look at the corresponding read in the fastq file, it looks like this: @fasta_02:23:B02CBACXX:8:2315:2667:7273 1:N:0:GATCAG

And iu-remove-ids-from-fastq expects: fasta_02:23:B02CBACXX:8:2315:2667:7273 1:N:0:GATCAG

Even though to my understanding the read name fasta_02:23:B02CBACXX:8:2315:2667:7273 is unique.

Could this behavior be modified?

Thank you!

meren commented 5 years ago

Dear Alon,

Thank you very much for your comments. The developers are thrilled to hear that you are happy with this modest tool.

If you don't mind generating an example set, we would be happy to do our best to offer a solution.

Best wishes,