How does IGB provide strand specific output

Question

[nagamalaimohan]

I want to know on what basis IGB separates the reads into forward and reverse strand and is there anyway to generate strand specific bed file output for a set of coordinates.

[Carlo Yague]

In what format is your input ?

[vimlakany]

I wish to know when i give sorted .bam file as input file. How does IGB separate the reads into + and - strand? can i use it to look for antisense transcription?

Answer 1

[Carlo Yague]

How does IGB separate the reads into + and - strand?

The alignment file (bam or sam) countains flags that tell you if the read is mapped on the reverse or forward strand. More info on this related post.

Can I use it to look for antisense transcription?

Short answer, yes. For instance if you use featureCounts to quantify the number of reads per genes, you can play with the -s option to count reads mapping in anti-sense of genes.

Is there anyway to generate strand specific bed file output for a set of coordinates ?

Yes, with bedtools bamtobed for instance.

[vimlakany]

It worked. Thank you so much.

[vimlakany]

How to generate 12 column bed file using bedtools or coverageBed?

[harold.smith.tarheel]

This question is completely unrelated to the original one. Please submit as a new post with appropriate title. See this post for guidance.