8 results in 0.0029 seconds.
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How does BWA identify PCR duplicates correctly?
Does it use the usual "same-start-position-for-both-paired-ends" approach? If so, why do many users do this check manually or use picard and... -
tophat : sam-flag 115 = properly-paired + read.reverse + mate.reverse ?
cross posted on biostars: http://www.biostars.org/p/87071
I ran tophat2 using the standard options.
...Code:$ tophat2 -v
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picard SamToFastq error in umapped reads which MAPQ is not 0
Hi,
SamToFastq.jar will be stop when it meet the unmapped reads which flag is 4 or 20 but the MAPQ is not 0. Picard is not so smart,it couldnot...Last edited by upper; 12-05-2012, 05:33 PM. -
flag inside sam file
I got a read aligned as below:
HWI-1KL138:2:2105:12847:125331#GCCAATGCCAAT 161 chr1 12036 1 74M = 12645 1188 ... -
SAM flag forward/reverse first/second
Hello,
I am a little confused with the interpretation of SAM flags
From http://ppotato.wordpress.com/2010/08...wise-flag-pair... -
Sam flags for bwa-aligned paired end reads with identical + / - strand coordinates
I'm looking at some paired end WGS data from a library with very small insert sizes, meaning that many of the DNA fragments are sequenced fully in both... -
Is * really a valid value for a SAM FLAG field?
The SAM spec (v1.3-r882, page 3) states that * is a valid value for the SAM FLAG field, yet the table just above it indicates that it is an int in the... -
sam flag 97 and 145
Hello,
After alignment, I got reads in the sam format with flag 97 and 145.
flag 97:
the read is paired in sequencing;...
