Visualize Strand-Specific Rna-Seq : How To Differentiate Strands
5
5
Entering edit mode
11.7 years ago

Hi,

I wonder how to display such a figure ( the green coverage). So how differntiate the sens coverage from the anti-sens coverage ? I search in IGV options but I didn't find anything ...

enter image description here

Thanks a lot

N.

rna-seq visualization strand • 15k views
ADD COMMENT
2
Entering edit mode

One possible workaround would be to split the bam file by strand and load each separately.

ADD REPLY
3
Entering edit mode
10.4 years ago
Ann ★ 2.4k

IGB bioviz.org) can display different strands data in different tracks. To separate plus and minus strand alignments into two tracks, select the track, select Annotation tab, and deselect the combine strand option ( +/- ) in the section labeled "Strand." It can also color-code the data by strand. Here's an image to illustrate:

https://www.dropbox.com/s/sp7zqat7r2n568u/SeparateStrands.png

ADD COMMENT
0
Entering edit mode

this is why I like IGB..

ADD REPLY
2
Entering edit mode
11.7 years ago

As far as IGV is concerned, I believe that it does not have this feature (yet).

If you want to use other tools, the bioconductor package Gviz has an AlignedReadTrack which plots stranded coverage data in a similar fashion to the green chunk of the image you posted above.

ADD COMMENT
2
Entering edit mode
11.7 years ago
Geparada ★ 1.5k

One simple way to do this on any visualization program it's just pre-filter the SAM/BAM by strand, and put the reads that aling to minus or plus strand in two different files. Then, you can visualize the coverage of both strand by separate.

ADD COMMENT
0
Entering edit mode

I tried with samtools but it seems not to be ok :

for positive strand

samtools view -F 0x10 -b input.bam > postiveStrand.sam

for negative strand

samtools view -f 0x10 -b input.bam > negativeStrand.sam

ADD REPLY
0
Entering edit mode

make sure to use the right flag, and you can just use integers 16 in this case see http://picard.sourceforge.net/explain-flags.html

ADD REPLY
0
Entering edit mode

What I want to do is to extract the reads (and its pair) where the first-in-pair (so coming from the R1 fastq file) aligned to the reverse strand . Is that possible ?

ADD REPLY
0
Entering edit mode

See this cool tutorial by Istvan Albert.

ADD REPLY
0
Entering edit mode
9.4 years ago
wm ▴ 560

@Ann How can I show the strand-specific reads? This fig seems not a strand-specific alignment (both strand have almost the same reads).

ADD COMMENT
0
Entering edit mode
8.7 years ago
jerry ▴ 130

If you have paired-end reads, then just splitting the BAM file into forward and reverse strand BAM files using samtools view will NOT work. All this will do is place all forward 'mate' reads on the forward strand, and reverse mate reads on the reverse strand, which is not what you want. You want to know which paired-end ALIGNMENTS (not reads!) map to the forward strand, and which alignments map to the reverse strand. Unfortunately, this information is hard to extract from the BAM file, and IGV does not have this feature yet.

ADD COMMENT
0
Entering edit mode

so how to do it? any idea.

ADD REPLY
0
Entering edit mode

Very interested here too ! Did someone make any progress on this question ?

ADD REPLY

Login before adding your answer.

Traffic: 1776 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