Question: Extract fastq sequences from BAM with flag Supplementary alignment
gravatar for devillartay
2.2 years ago by
devillartay30 wrote:

Dear all, after running BWA-MEM on a fastq dataset, I identified some "supplementary alignment" reads with Flag 2048 corresponding to chimeric reads. I desperately try to find a way to extract those reads from my dataset into a new fastq file for further analysis. Thanks for your help (I am not an expert in Galaxy)

fastq sam flag filter bam • 1.0k views
ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson25k • written 2.2 years ago by devillartay30
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


First, convert the BWA-MEM output with BAM-to-SAM without outputting the SAM header. Next, use Filter on the second column with the value as "2048". Check this output to see if only the target sequences remain and make sure that the database metadata is assigned (click on the pencil icon to assign if needed). Then as the last step extract the sequences with SamToFastq.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson25k

Thanks for your help. everything worked and I indeed get the fastq files of the filtered "2048" reads in the (UNPAIRED READS) output of SamToFastq. The problem is that it is the sequence of the aligned reads trimmed of the non aligned part (half of the chimeric read) In fact I would like to recover the initial full length read which was subsequently tagged "2048" and not the trimmed sequence I'm not sure I'm clear enough on this....... Best. JP

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by devillartay30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour