Hi everyone,
So I am doing 100 bp PE reads, and I want to trim off the first 15 bp's. I want to do this because when I check the distribution of GCTA, they vary quite a bit between the first 15 bp's, but then are all 25% after that. Although the Phred Score is still quite high (above 30), a Tech Support person at Illumina mentioned that I would probably get better results by trimming it.
I noticed that with tophat, you cannot use an option telling it to start at the 15th base, so the only option appears to be trimming. I tried to use fastx_trimmer, but it appears to be taking a LONG time, and I can only get it to do one file at a time. Is there another software that would be faster, or another way of going about this? Also, can I do more than one at a time?
Thanks so much for any advice!
So I am doing 100 bp PE reads, and I want to trim off the first 15 bp's. I want to do this because when I check the distribution of GCTA, they vary quite a bit between the first 15 bp's, but then are all 25% after that. Although the Phred Score is still quite high (above 30), a Tech Support person at Illumina mentioned that I would probably get better results by trimming it.
I noticed that with tophat, you cannot use an option telling it to start at the 15th base, so the only option appears to be trimming. I tried to use fastx_trimmer, but it appears to be taking a LONG time, and I can only get it to do one file at a time. Is there another software that would be faster, or another way of going about this? Also, can I do more than one at a time?
Thanks so much for any advice!
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