I have 10 .sam
files after my bowtie2
alignment on ten single-pair sequences. I would like to build a graph based on that output data, however I don't see any other solution but just writing the alignment percentage manually after each iteration.
Is there a tool that can help me to build a .csv
file so I can manipulate the output data more easily?
bowtie2 ‹args› | samtools sort --output-fmt-option level=0 | samtools view -b -o sorted.bam
(this immediately sorts the BAM file, which requires a lot of RAM; if this isn’t suitable for you, omit the intermediate step; but you normally want to have sorted BAMs). $\endgroup$