bowtie reporting reads that did not align

Question

[sumithrasank75]

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

[Ashutosh Pandey]

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.

Answer 1

[Sukhi Singh]

How To Filter Mapped Reads With Samtools