Genomic regions to plot in strand-specific

[tamarsegal]

Hello I use your wonderful tool in order to plot the signal around the promoter regions. I'm wondering if there is an option to take the strand information into consideration. For example if I have a location in the bed file which comes from the minus strand, I would like the "upstream" region to be to the right side of the location instead of the left side. As I understand, the "-SS" parameter only refer to the reads in the BAM file. My sequence data was not strand specific, so I want all reads to be used in the analysis, but I do would like the "upstream" and "downstream" regions to be calculated based on the strand. Is it possible? Looking forward to your reply Thanks Tamar

[brianpenghe]

I wish they can also distinguish sense and antisense strands

[tamarsegal]

I found out how to do it. You should use BED format, when column 6 has the information about the strand, it works. Good luck :)

[brianpenghe]

You sure it works? Any sample figures to post here?

[Rseq]

I've tried without any success using the following the command:

cd "$dir_metaplot"
echo "file1_for.bam -1  \"sense\"   75  bisque4
file1_rev.bam   -1  \"anti-sense\"  75  seagreen4
file1+RNA_for.bam   -1  \"sense+RNA\"   75  sienna4
file1+RNA_rev.bam   -1  \"anti-sense+RNA\"  75  orangered3
" > "$dir_scripts"/config.txt

/anaconda3/bin/ngs.plot.r -G hg19 -R TSS -D refseq -C "$dir_scripts"/config.txt -O "$dir_metaplot"/TSS -L 5000 -BOX 0 -VLN 0 -XYL 1 -SS both -P 0

I also did for genebody and with my own bed file with and without strands in the 6th column. Any ideas what could it be?

I used bowtie2 to map and selected forward and reverse reads with samtools:

  samtools view  -b -h -F 4 -f 16 -o file_rev_strands.bam $file_both_strands.bam
  samtools view  -b -h -F 4 -F 16 -o file_for_strands.bam $file_both_strands.bam

I sorted and indexed later with samtools and the bedgraph looks fine, but the metagene doesn't Any idea will be appreciated.