Hi everyone,
I am performing WES analysis using bowtie2. Actually I am trying to find out whether specific sequences are present in patients genome. I work with paired-end sequencing, the length of read is 100. I see that sometimes there are cases when read fragment (e.g. length of 19, CIGAR 19M) get maximum MAPQ (42) in my alignment. What happened to the remaining part of read? I did not set --local mode, I only specify input and output files. How is this possible? Is there a possibility to avoid such cases using bowtie2 parameters? I am afraid that these reads do not really reflect the presence of my sequences in the genome.
Thank you in advance!
What settings did you use? What you're describing shouldn't happen with the default settings.
Here is my script: bowtie2 -x junctions.index -p 8 -1 filename_end1.fastq -2 filename_end2.fastq -S output.sam
Most of the lines in my output.sam look fine, but some of them look like this:
Some of my sequences I am looking for are rather short and I am not expecting the second read in a pair to map the same sequence. Can this issue occur because I am treating paired-end sequencing like this?
the alignment that you list above is not a fragment, it is a full read match note
19M
nothing was clipped off.You have a mismatch in that
19M
but that's about it.Does this mean that the original read is the length of 19? Is this possible? I was also wrong in the beggining, I am working with WES, not WGS, maybe this is essential
Your data must have been trimmed.