User: miguelcamachosanchez

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Posts by miguelcamachosanchez

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Comment: C: Filter reads with most frequent mapping coordinates from BED
... Thanks a lot for your input. It actually did work perfectly! I integrated it into my pipeline to finally filter the corresponding reads from my original BAM file: bedtools intersect -a sorted.bed -b to_keep.bed -sorted -f 1.0 -F 1.0 | sort -k1.16,1n | awk '{print $4}' > reads java -jar p ...
written 7 months ago by miguelcamachosanchez0
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Filter reads with most frequent mapping coordinates from BED
... My bed file is like: head -n3 test.bed Contig_68 1 53 HISEQ:244:C9PLYANXX:6:1101:2559:2541 60 + Contig_68 2 53 HISEQ:244:C9PLYANXX:6:1102:15469:35000 60 + Contig_68 1 53 HISEQ:244:C9PLYANXX:6:1102:15983:77622 60 + Contig_68 1 53 HISEQ:244:C9PLYANXX:6:1102:15114:7 ...
bed next-gen radseq assembly written 7 months ago by miguelcamachosanchez0 • updated 7 months ago by ATpoint19k

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