User: bioinfo89
bioinfo89 • 40
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Posts by bioinfo89
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... Hi All,
I get this error when I run the ChIPQC package on my data (single sample). The commands are mentioned below:
## Load sample data
samples <- read.csv('meta/samplesheet.csv')
#View(samples)
## Create ChIPQC object
chipObj <- ChIPQC(samples, annotation="hg19")
...
written 8 days ago by
bioinfo89 • 40
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... Yes I did compress it. But the output works fine. ...
written 5 weeks ago by
bioinfo89 • 40
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... seqtk sample -s100 SRR_1.fastq 0.1 >R1_1_sub0.1.fastq
seqtk sample -s100 SRR_2.fastq 0.1 >R2_2_sub0.1.fastq
####Running ChIA-PET2 :
ChIA-PET2-0.9.3/bin/ChIA-PET2 -t 10 -g hg19.fa -b hg19.chrom.sizes -f R1_1_sub0.1.fastq.gz -r R2_2_sub0.1.fastq.gz -m ...
written 5 weeks ago by
bioinfo89 • 40
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... Hi All,
I am using ChIA-PET2 tool to process the data. I am subsampling reads (0.1 to 0.9) using seqtk and running the ChIA-PET pipeline and I get the following error:
ERROR: The input file is neither a BAM file nor a SAM file.
I checked the sam files they appear to be fine (using Picard Vali ...
written 5 weeks ago by
bioinfo89 • 40
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... Yes I resolved it. Thanks! ...
written 4 months ago by
bioinfo89 • 40
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... Yes it is the actual executable and it has execute permissions. ...
written 4 months ago by
bioinfo89 • 40
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... It did not throw any errors as such. I guess I should have mentioned the dir path for dep_dir, I think I missed that. Now it makes more sense why I am getting this error. I'll try to install it again.
Thanks @genomax! ...
written 4 months ago by
bioinfo89 • 40
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... Right ok.
There are no sub dir under /scratch/krc190002/WGS_tools/ChIA-PIPE/samtools ...
written 4 months ago by
bioinfo89 • 40
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... echo $PATH
/opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin:/opt/ohpc/pub/compiler/gcc/8.3.0/bin:/opt/ohpc/pub/utils/prun/1.3:/opt/ohpc/pub/utils/autotools/bin:/opt/ohpc/pub/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/krc190002/scratch/WGS_tools/bedtools2/bin:/home/krc190002/scratc ...
written 4 months ago by
bioinfo89 • 40
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... Yes, I did set the $PATH to the location of the programs.
I mean that the modules are present in the ChIA-PIPE folder as suggested by the installation guide. I am just running the shell script of the tool which is using these modules:
### 5) Uncomment below to module load dependencies
mo ...
written 4 months ago by
bioinfo89 • 40
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