User: myology

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myology0
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Posts by myology

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Comment: C: Difference in BAM coverage between bedtools output and IGV coverage track
... DNA, single pair, not strand-specific... ...
written 9 weeks ago by myology0
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Comment: C: Difference in BAM coverage between bedtools output and IGV coverage track
... Thanks, I'm going to look into this... ...
written 9 weeks ago by myology0
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Comment: A: Difference in BAM coverage between bedtools output and IGV coverage track
... I could see how coverage metrics for a given position would be different if BAMs are generated differently. However, in my case it's the same BAM. So I don't really understand why I see 15 reads in IGV at a certain position, but bedtools tells me there are 19... ...
written 9 weeks ago by myology0
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Comment: A: Difference in BAM coverage between bedtools output and IGV coverage track
... $bedtools genomecov -ibam IonXpress.bam -bga > test-genomecov.bed $wc -l test-genomecov.bed 8631278 $awk '$4<20' test-genomecov.bed > less20x-genomecov.bed 3705841 $sort -k1,1 -k2,2n my-regions.bed > my-regions-sort.bed $bedtools intersect -a less20x-genomecov.bed -b my-regions-sort.bed ...
written 9 weeks ago by myology0
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Difference in BAM coverage between bedtools output and IGV coverage track
... Hi, I’m using bedtools to find regions of<20x coverage of target areas for a .BAM generated by IonTorrent server. The result obtained is different from the coverage track in IGV for a given .BAM – often a couple of reads more for a given position obtained by bedtools. Thus, my regions of <20x ...
bedtools iontorrent bam written 10 weeks ago by myology0 • updated 6 weeks ago by Biostar ♦♦ 20

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