Fastq Screen shows many unmapped reads
0
0
Entering edit mode
7 weeks ago
esimonova.me ▴ 20

I performed fastq_screen analysis of human tumor samples and it looks like that either READ1 or READ2 show high number of unmapped reads. I received the data from a vendor and I try to figure out what causes this behavior?

enter image description here

fastq_screen • 155 views
ADD COMMENT
0
Entering edit mode

check the qualities of the reads (poly-NNN ?) , pick a few unmapped reads and run NCBI blast.

ADD REPLY
0
Entering edit mode

Poly-N content is fine, no N were called . I will pick them in the next step as fastq_screen doesnt generate BAM files

enter image description here

ADD REPLY

Login before adding your answer.

Traffic: 1923 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6