Hi all,
I have a little problem with bowtie2 aligner related to the quality of my reads in fastq file. I have some raw RNAseq data (Illumina, single end, 50pb), and when I try to align it against my reference sequence, it pops me after a while messages like "read HWI-ST766:125........ has more quality values than read characters" or ""read HWI-ST766:125........ has spaces in quality check".
So, obviously, there are some reads in my file that are "corrupted" in some way and bowtie2 doesn't like that.
I tried to delete these specific line with grep and sed functions, it worked well but it's too long and I can't do it every time I have this issue.
So, I was wondering if I could somehow clean my data according to the quality or perhaps eliminate all reads which will make bowtie2 bug...
Anyone has a clue how to do this? It's frustrating, cause I feel I'm not far away from getting my results, but there is always something else!
Here is my command for alignment (if it can help):
bowtie2 -q -a -p 6 -t -x IndexFile -U FastqFile -S SamFile
Thank you in advance!
I have a little problem with bowtie2 aligner related to the quality of my reads in fastq file. I have some raw RNAseq data (Illumina, single end, 50pb), and when I try to align it against my reference sequence, it pops me after a while messages like "read HWI-ST766:125........ has more quality values than read characters" or ""read HWI-ST766:125........ has spaces in quality check".
So, obviously, there are some reads in my file that are "corrupted" in some way and bowtie2 doesn't like that.
I tried to delete these specific line with grep and sed functions, it worked well but it's too long and I can't do it every time I have this issue.
So, I was wondering if I could somehow clean my data according to the quality or perhaps eliminate all reads which will make bowtie2 bug...
Anyone has a clue how to do this? It's frustrating, cause I feel I'm not far away from getting my results, but there is always something else!
Here is my command for alignment (if it can help):
bowtie2 -q -a -p 6 -t -x IndexFile -U FastqFile -S SamFile
Thank you in advance!
Comment