Question: Exome data : drawing a plot showing GC content against normalized mean
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gravatar for pegeot.henri
7 days ago by
pegeot.henri0 wrote:

Hi, I wonder what should I do to obtain a dataset to draw a plot showing GC content against mean depth for exome data (like this). I have bam files, bed files, fastQ files but I don't even know where I should start.

Thanks

gc content exome • 79 views
ADD COMMENTlink modified 6 days ago • written 7 days ago by pegeot.henri0
2

see Plot Coverage Vs. Gc Content for a start

ADD REPLYlink written 7 days ago by Pierre Lindenbaum120k

Is CollectGcBiasMetrics (Picard) what I am looking for ?

ADD REPLYlink written 7 days ago by pegeot.henri0
0
gravatar for pegeot.henri
6 days ago by
pegeot.henri0 wrote:

So I have done the following :

  • Using bedtool nuc I have calculated the GC content of each region of my bed file

  • Using samtools bedcov, I have calculated the average depth of coverage for each region of my bed : samtools bedcov -Q 30 Intervals.bed sample.bam | sort -k1,1 -k2,2n -k3,3n | awk 'BEGIN {OFS="\t"}{a=($3-$2+1);b=($5/a);print $1,$2,$3,$4,b,"+","+"}' > sample_coverage.tsv

  • Using bedtools intersect or a simple join you can have the data to draw a plot depth ov coverage Versus GC content (%)

ADD COMMENTlink modified 6 days ago • written 6 days ago by pegeot.henri0
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