Question: bowtie reporting reads that did not align
0
gravatar for sumithrasank75
5.1 years ago by
United States
sumithrasank75140 wrote:

Is there an option in bowtie to get a list of reads that did not align to the reference. Thanks

alignment next-gen • 1.3k views
ADD COMMENTlink modified 5.1 years ago by Sukhdeep Singh10k • written 5.1 years ago by sumithrasank75140

If you used bowtie with default settings, the unaligned reads should be present in the output (SAM) file. You can use "samtools view -f4" command to extract unmapped reads. You can then convert bam to fastq file or simply get the read names. Read the samtools manual for more help.

 

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Ashutosh Pandey12k
1
gravatar for Sukhdeep Singh
5.1 years ago by
Netherlands
Sukhdeep Singh10k wrote:

A: How To Filter Mapped Reads With Samtools

ADD COMMENTlink written 5.1 years ago by Sukhdeep Singh10k
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