Does anyone have a conversion tool for .sam format to .wig format? I need to visualize my aligment data on ucsc.
Thanks!!
Thanks!!
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In Unix/Linux, a one-liner could do this for you:
samtools pileup -S -f <reference fasta> <sam file> | awk '{print $1, $2-1, $2, $4}' > mywiggle.bed
--Nancy -
Nice! BTW it creates a huge wig file as it gives a value for each position.
I would post-process the data with some binning tool (such as wig2bdg included in MACS). As example:
bam file with ~12000000 aligned reads -> 1.7 Gb compressed wig -> 87 Mb compressed binned bedgraphComment
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nhansen:
I follow your methods and samtools show "[bam_plp_destroy] memory leak: 1. Continue anyway."
Dose it mean I don`t have enough memory?Comment
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