what is difference between -i and -ibam in genomCoverage?
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2.8 years ago
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I like to convert the BAM file to BIGWIG format I used bedtools genomeCoverage to change BAM to BEDGRAPH but I do not know difference between below comands: bedtools genomecov -bg -ibam and bedtools genomecov -bg -i -g hg19.genome because when I use the second one I faced with this ERROR:

Unexpected file format. Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 808727866?

but the first one works well.

Also, I used deeptools bamCoverage to change BAM to BEDGRAPH but there is no data for its output when I opened it in the UCSC.

bedtools deeptools bamCoverage genomeCoverage • 771 views
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Entering edit mode
2.8 years ago
ATpoint 55k
-i <bed/gff/vcf>
-ibam       The input file is in BAM format.
            Note: BAM _must_ be sorted by position

Pretty self-explainatory, no? -i accepts bed/gff/vcf and ibam accepts BAM.

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