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Hi all,
Basically, I'm wondering if tophat2 (calling bowtie2) can align paired reads from two different files that don't have the same number of reads? Right, that sounds a bit vague, but in a nutshell;
I have gotten raw read files in FASTQ format back from an RNA seq project. This is from paired end sequencing. So for a single lane there are 2 files (one for each pair) and both have 29181932 reads. I then trimmed each read for a quality score, but when I was doing this I included an option to remove reads that, after trimming, contained less than 25 bps (These are 40bp reads). More reads were removed, because of this, from the second mate of the pair. Now I have different numbers of reads for each pair (pair 1 29081810; pair 2 26989485). A difference of about 2.1 million reads, but this is expected as quality is always lower on the second mate.
The problem now is that I don't know if bowtie2 will only align reads for which the 2 corresponding mates exist or will it align each read independently? Preferably the former.
I know I could create files with only the IDs that are in both, but I don't want to do this if bowtie2 will take care of it for me.
Any advice would be greatly appreciated.
Basically, I'm wondering if tophat2 (calling bowtie2) can align paired reads from two different files that don't have the same number of reads? Right, that sounds a bit vague, but in a nutshell;
I have gotten raw read files in FASTQ format back from an RNA seq project. This is from paired end sequencing. So for a single lane there are 2 files (one for each pair) and both have 29181932 reads. I then trimmed each read for a quality score, but when I was doing this I included an option to remove reads that, after trimming, contained less than 25 bps (These are 40bp reads). More reads were removed, because of this, from the second mate of the pair. Now I have different numbers of reads for each pair (pair 1 29081810; pair 2 26989485). A difference of about 2.1 million reads, but this is expected as quality is always lower on the second mate.
The problem now is that I don't know if bowtie2 will only align reads for which the 2 corresponding mates exist or will it align each read independently? Preferably the former.
I know I could create files with only the IDs that are in both, but I don't want to do this if bowtie2 will take care of it for me.
Any advice would be greatly appreciated.
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