Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
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nginet • 0
@nginet-15664
Last seen 3.4 years ago

Dear all,

As a start I must confess that I am not really trained in bioinformatics. I managed to use bowtie2 and some samtools embedded in RStudio to align Illumina reads to a reference genome. I wish now to write into 2 separate files (to be converted in fastq) the mapped and unmapped reads. I need to perform a de novo assembly with the unmapped reads. Can anyone suggest a script that I can copy and adapt to my needs ?

Many thanks

Nico

R sequencing alignment rsamtools mapping • 907 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

https://www.biostars.org/p/56246/
 

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