estimate Mean Inner Distance between
Mate Pairs
Howdy Jianguang,
There's a more complete description of the SAM format in "The Sequence
Alignment/Map format and SAMtools", Li et al, Bioinformatics (2009). And
you can find the latest specification for the format at
samtools.sourceforg
Howdy Jianguang,
There's a more complete description of the SAM format in "The Sequence
Alignment/Map format and SAMtools", Li et al, Bioinformatics (2009). And
you can find the latest specification for the format at
samtools.sourceforge.net .
In the spec, the terminology for the ISIZE field has
Hello Jianguang,
On the Bowtie tool form itself, please find this text:
Outputs
The output is in SAM format, and has the following columns:
Column Description
1 QNAME Query (pair) NAME
2 FLAG bitwise FLAG
3 RNAME Ref
Dear All,
In order to figure out the Mean Inner Distance between Mate Pairs of my
paired-end RNA-seq datasets, I ran Bowtie (Map with Bowtie for Illumina) with
both forward and reverse datasets and mouse mm9 as reference genome. Below I
list the Bowtie output for only one pair of reads (I put t
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