Using ReadDepth for non-human data

Question

[misbahabas]

hello,

I am using readDepth tool , for this i need annotation files of non human genome, I am following readme from site "https://xfer.genome.wustl.edu/gxfer1/project/cancer-genomics/readDepth/index.html " but there is error

  Use of uninitialized value $ARGV[5] in concatenation (.) or string at mapAndGc.pl line 78, <GEN1> line 8438174.

Use of uninitialized value in concatenation (.) or string at mapAndGc.pl line 78, <GEN1> line 8438174. Can't open output file.

gzip: /.gc: No such file or directory

gzip: /.map: No such file or directory

Kindly tell me how to resolved it , Thanks :((

[agata88]

I don't know readDepth tool but the error is quite simple. You have not specified input or output file directory. The first line "Use of uninitialized value ..." looks like warning. Please copy a command to the post so we can see where you've made a mistake, best, Agata

[misbahabas]

Thankx for reply

I used this script

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

perl mapAndGc.pl ~/path to dir/outdir/chr1.sam canfam3.1.genome  $windowSize $chr $readLength $outdir

gzip $outdir/$chr.gc

gzip $outdir/$chr.map

rm -f $outdir/$chr.sam

Answer 1

[Chris Miller]

Without more information, I'm afraid that I can't help you. The scripts provided are short and straightforward. Your error relates to not being able to find specific files that it expects to be there. Make sure all preceding steps have completed successfully. If you go line by line through the process, verifying that your inputs and outputs from each step look sane, I imagine you'll figure out what's happening.

Answer 2

[misbahabas]

Actually 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

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

thankx