tophat2 bowtie option help

[akh22]

Hi,

I am using Tophat2 on the grid and trying to get single and paired read unmapped bam files by a following command;

tophat2 -p 16 -o 4560_output -G ~/GRCh37_73.gtf ~/Bowtie2Index2/Ensemble 4650_R1merged.fastq 4650_R2merged.fastq --b2-un-conc ~/4560_output/pefailed.bam --b2-un ~/4560_output/singlefailed.bam

But I only get unmapped.bam but not pefailed.bam and singlefailed.bam. I really appreciate any help with this.

Thanks in advance.

[dpryan]

"--b2-un-conc" and "--b2-un" aren't options for tophat2. They look like bowtie2 options with "b2-" slapped on the front. That simply won't work as I don't think there's a way to get tophat to do that without hacking the source code a fair bit. However, it would be relatively straight-forward to simply extract that from the unmapped.bam file, which should be name-sorted.

[akh22]

Hi Devon,

I am new to Samtools. Could you send me a pointer of command that do these ?

Thanks.

Aki

[dpryan]

Hi Aki,

I don't have any paired-end data aligned with tophat2 at my finger-tips, but I imagine if you "samtools sort -n unmapped.bam" to ensure that the file is name-sorted, you would then be able to write a small script (in python/perl/whatever) to then print out reads that either do or do not have a mate (i.e., read with the same name).