GC content from bam to fasta file
I want to get mean_gc content of a given bed regions from a bam file
I use
samtools fasta $bam > $bam.fasta
bedtools nuc -fi $bam.fasta -bed $regions.bed >$bam_gc_content.bed
this gives me the error 1:67000041-67000044) beyond the length of chr1 size (0 bp). Skipping.
my regions.bed looks like this
1 27719 30282
1 34575 35119
1 178413 180107
1 196349 196596
1 198074 200761
fasta file bam file (paired end)
>HWI-D00309:105:C7HAGANXX:1:2104:19269:80273/2
AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
>HWI-D00309:105:C7HAGANXX:1:2212:13536:55714/1
CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
>HWI-D00309:105:C7HAGANXX:1:2307:16222:92746/2
ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
>HWI-D00309:105:C7HAGANXX:1:1210:15413:21872/2
AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG
>HWI-D00309:105:C7HAGANXX:1:1313:15716:47136/1
CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
>HWI-D00309:105:C7HAGANXX:1:2104:19269:80273/1
TGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG
>HWI-D00309:105:C7HAGANXX:1:2212:13536:55714/2
TGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG
>HWI-D00309:105:C7HAGANXX:1:2307:16222:92746/1
TGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG
>HWI-D00309:105:C7HAGANXX:1:1313:15716:47136/2
GTTTGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT
>HWI-D00309:105:C7HAGANXX:1:1105:12543:6619/1
CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAGGACC
>HWI-D00309:105:C7HAGANXX:1:1210:15413:21872/1
TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAAC
>HWI-D00309:105:C7HAGANXX:1:2202:2887:84643/1
How do i resolve this issue?
1 answer
Your bam.fasta file is now essentially original reads converted to fasta format. How can bedtools correlate them with your regions.bed file which contains chromosomal identifiers?
You should extract reads that span the intervals with samtools view first (A: Extract Reads From A Bam File That Fall Within A Given Region ) and then convert them to fasta for GC analysis.
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