It worked. Thank you so much.
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How does IGB provide strand specific output
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.
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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 ?
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In what format is your input ?
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?