Problem in generating GCWinds and MAPPBILITY files for readDepth
0
0
Entering edit mode
7.0 years ago
misbahabas ▴ 70

Hello

I used "createCustomAnnotations" scripts from here for non human data: https://xfer.genome.wustl.edu/gxfer1/project/cancer-genomics/readDepth/index.html

I have bam files and reference genome, so I convert bam file into sam file and run only last command of

runEachchr.sh !/gsc/bin/bash arguments

chr=chromosome37 readLength=100 fastaDir=$3 outdir=outdir windowSize=100

generate all possible reads of the given size from that chromsome

perl allSeq.pl $fastaDir/$chr.fa $readLength > $outdir/$chr.fastq align those reads using bwa bwa aln -t 4
$fastaDir/all_sequences.fa $outdir/$chr.fastq >$outdir/$chr.aln.sai bwa samse -n 1 
$fastaDir/all_sequences.fa $outdir/$chr.aln.sai $outdir/$chr.fastq >$outdir/$chr.sam clean up rm -f 
$outdir/$chr.fastq $outdir/$chr.aln.sai

I USED THIS COMMAND ONLY

convert the sam file to a mapability and gc-content tracks

perl mapAndGc.pl /home/misbah/InstalledUtilites/Dogsd_bamfiles/outdir/chr37.sam canfam3.1.txt 
$windowSize $chr $readLength $outdir gzip $outdir/$chr.gc gzip $outdir/$chr.map rm -f $outdir/$chr.sam

but it give error

Use of uninitialized value $len in division (/) at mapAndGc.pl line 83, <gen1> line 2097423.

I am in trouble, please tell me about this issue

if I changed in chr list file

like

chr1 122678785 2
chr2 85426708 2
chr3 91889043 2
chr4 88276631 2

it give no error but gc and map file have 0 and NA values . it not give proper output please tell me about it .. I am so worried about it :(

Thanks in advance

genome cnv • 1.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 2037 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6