Samtools: remove unmapped reads as well as reads that are mapped incorrectly
Hello, I have to remove unmapped reads and mapped incorrectly reads by using samtools view. I have found in the internet and in samtools view manual, to do that I have to use options -F and -q. But I don't understand how people decide to use, for example, -F 4 -q 10 or -F 8 and so on. On what I have to base on, then I want to chose "power" of options?
• 582 views
•
link
updated
by
Ram
•
written
by
npavliukovec •
•
written
by
npavliukovec •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
bam file: unmapped but matching reads (samtools view -f 4)
written by Tommy •
-
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that …
written by Jalil Sharif •
-
Samtools mapped and unmapped flags, what is the difference between the flags?
written by DNAngel
-
Get all unmapped read and mate in bam
written by vinaykusuma •
-
Trying to understand samtools -f and -F
written by shibl_a •
-
FASTQ exctract ID's
written by User000
-
Identification of the sequence insertion site in the genome
written by valerie
-
Do I need to remove unmapped reads before running MACS2?
written by bxia
-
filter mapped and unmapped bam file
written by mgadrianam •
-
Is correct finding unique reads with the flag -F 0x104?
written by miquinhap •
