Output unmapped reads to a file when using tophat2

Question

[biolab]

Hi, everyone,

I am using tophat2 for reads mapping. I know there is a--un option in bowtie2 to write unmapped reads to a file. However, I don't know if tophat2 has similar option (at least I did not find this option in the manual). Could anyone who has expertise on mapping give me a solution?

Another question I want to raise is: can I set large intron size? The default --max-segment-intron option is set to 500,000, if I increase it to 10,000,000, will this decrease speed a lot?

Thank you very much for any of your suggestions!

Answer 1

[iraun]

• Question 1. Tophat2 output has a file named unmapped.bam which contains unmapped reads, is this what you are looking for?
• Question 2: I guess that the speed should not be affected very much, but I've never try a value such high as 10,000,000. I think that the only solution is to try and see. Sorry if this is not the answer you would like to have :).

[biolab]

Hi airan,

Thanks a lot for your answer. For Question1, actually I did not mean unmapped.bam. I want to get a fastq file. Anyway, I can retrieve the reads ids, and then get sequences. For Question2, I agree to try it. Thanks.