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how_to [2022/08/04 16:54] – [Add only modified changes and ignore untracked files using git.] adminhow_to [2022/08/10 02:20] – [Run simultaneous jobs (on multiple files) in a single mpi on a cluster?] mohsen
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 This is a collection of short answers and links to some miscellaneous questions that we have had while doing research in Oncinfo. This can also be a useful resource for other scholars in the field of computational biology with similar interests and challenges. This is a collection of short answers and links to some miscellaneous questions that we have had while doing research in Oncinfo. This can also be a useful resource for other scholars in the field of computational biology with similar interests and challenges.
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 +
 +==== Extend   bam  reads to a fixed fragment size to better view peaks with   igv   ====
 +
 +Assume you have ''input.bam'' which contains mapped short single-end sequence reads, but you know the fragment size=''100''. With the following command, you can make a bam file that have the extended reads, but you will miss the actual reads. This helps to better visualize the actual read signal:
 +<code>
 +bedtools bamtobed -i input.bam | \
 +awk -F'\t' 'BEGIN {OFS = FS} {if ($6=="+") {$3=$2+99} else {$2=$3-99}; if ($2<0) {$2=0}; print $0;}' | \
 +bedtools bedtobam -i -> extended_input.bam
 +</code>
  
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