Extracting Multiple Mapped reads from Bismark output

Question

[chaudharyc61]

Hello everyone

Bismark aligner gives a a report like :

• Final Alignment report

  Sequences analysed in total: 10000

  Number of alignments with a unique best hit from the different alignments: 6703

  Mapping efficiency: 67%

  Sequences with no alignments under any condition: 2232

  Sequences did not map uniquely: 1065

  Sequences which were discarded because genomic sequence could not be extracted: 0

So,How can I get the reads which are not mapped uniquely with their MAPQ scores and all (like from example 1065 reads)

Thanks Chandan kumar

Answer 1

[onestop_data]

I'm not familiar with Bismark, but here it says that the output can be in BAM format. If this assumption is true, you can use a script like this one to convert your BAM2FASTA only targeting the unmapped reads (See Only Unmapped sequences from BAM to FASTA)

I hope it helps.