Question: Visualize Strand-Specific Rna-Seq : How To Differentiate Strands
5
gravatar for Nicolas Rosewick
6.9 years ago by
Belgium, Brussels
Nicolas Rosewick8.5k wrote:

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.

visualization rna-seq strand • 9.3k views
ADD COMMENTlink modified 3.9 years ago by jerry10 • written 6.9 years ago by Nicolas Rosewick8.5k
2

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

ADD REPLYlink written 6.9 years ago by Istvan Albert ♦♦ 81k
2
gravatar for Steve Lianoglou
6.9 years ago by
Steve Lianoglou5.0k
US
Steve Lianoglou5.0k wrote:

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 COMMENTlink written 6.9 years ago by Steve Lianoglou5.0k
2
gravatar for Geparada
6.9 years ago by
Geparada1.4k
Cambridge
Geparada1.4k wrote:

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 COMMENTlink modified 6.9 years ago • written 6.9 years ago by Geparada1.4k

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 REPLYlink modified 6.8 years ago • written 6.8 years ago by Nicolas Rosewick8.5k

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 REPLYlink written 6.8 years ago by Istvan Albert ♦♦ 81k

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 REPLYlink written 6.8 years ago by Nicolas Rosewick8.5k

See this cool tutorial by Istvan Albert.

ADD REPLYlink written 3.9 years ago by Carlo Yague4.8k
2
gravatar for Ann
5.6 years ago by
Ann2.3k
Concord NC USA
Ann2.3k wrote:

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 COMMENTlink modified 5.6 years ago • written 5.6 years ago by Ann2.3k

this is why I like IGB..

ADD REPLYlink written 3.9 years ago by Antonio R. Franco4.3k
0
gravatar for wm
4.6 years ago by
wm130
China
wm130 wrote:

@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 COMMENTlink written 4.6 years ago by wm130
0
gravatar for jerry
3.9 years ago by
jerry10
United States
jerry10 wrote:

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 COMMENTlink written 3.9 years ago by jerry10

so how to do it ? any idea.
 

ADD REPLYlink written 3.9 years ago by Chirag Nepal2.2k

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

ADD REPLYlink written 2.2 years ago by erwan.scaon720
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