How to extract mapping features of multiple samples in one output?

Question

[star]

I have a multiple samples and I run mapping with Bowtie2 for them and now I have .bam files. I have tried to run Multiqc to see how is mapping rate, duplication rate and other features but It did not work with bowtie output I think. I would like to know is there any graphical program like Multiqc for observing aligning features?

[Bastien Hervé]

If I remember well, in bowtie2 informations about the alignment (alignment rate, not aligned rate...) are in the standard output (terminal).

If you want to check reads quality, GC content... You will have to run a tool like fastqc on your data and use multiqc to compile them

[Pierre Lindenbaum]

but It did not work with bowtie output I think

what happened ?

Answer 1

[h.mon]

MultiQC doesn't extract information from the bam files, rather, it extracts from log files. Bowtie2 logs are output to stderr, you have to redirect them to a file and pass this file to MultiQC.

[Phil Ewels]

Correct! If you forget, you can always run samtools stats on your aligned BAM file, which will give you a file to feed to MultiQC for a % alignment plot.