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
