Convert Un-Indexed Sam File To Wig File
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9.5 years ago
lsvijfhuizen ▴ 90

Dear All,

I want to convert an SAM file without head to an wiggle file. Can anyone help me with this? I haven't that BAM files. Thank you!

sam wiggle • 2.5k views
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9.5 years ago
Fidel ★ 2.0k

You may want to see this link on how to convert a SAM file (without a header) to a bam file. Afterwards you can use the BEDtool genomeCoverageBed to obtain a bedgraph file (which is similar to a wiggle file and probably will suit your needs)

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9.5 years ago

Here (under software) is small sam2wig perl-script. It is not very memory efficient and/or fast, but my intention to write it was the normalization of multiple mapping reads, which cannot be done using samtools.

Feel free to try it.

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