User: bioinfo89

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bioinfo8940
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Posts by bioinfo89

<prev • 78 results • page 1 of 8 • next >
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Error in ChIPQC(samples) : Unable to process. Each bam file must be associated with at most one peakset.
... 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") ...
chip-seq written 8 days ago by bioinfo8940
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Comment: C: ChIA-PET2 ERROR: The input file is neither a BAM file nor a SAM file.
... Yes I did compress it. But the output works fine. ...
written 5 weeks ago by bioinfo8940
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Comment: C: ChIA-PET2 ERROR: The input file is neither a BAM file nor a SAM file.
... 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 bioinfo8940
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ChIA-PET2 ERROR: The input file is neither a BAM file nor a SAM file.
... 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 ...
chiapet written 5 weeks ago by bioinfo8940
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Comment: C: Chia-pipe cannot find the module pigz
... Yes I resolved it. Thanks! ...
written 4 months ago by bioinfo8940
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Comment: C: Chia-pipe cannot find the module pigz
... Yes it is the actual executable and it has execute permissions. ...
written 4 months ago by bioinfo8940
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Comment: C: Chia-pipe cannot find the module pigz
... 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 bioinfo8940
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Comment: C: Chia-pipe cannot find the module pigz
... Right ok. There are no sub dir under /scratch/krc190002/WGS_tools/ChIA-PIPE/samtools ...
written 4 months ago by bioinfo8940
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Comment: C: Chia-pipe cannot find the module pigz
... 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 bioinfo8940
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Comment: C: Chia-pipe cannot find the module pigz
... 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 bioinfo8940

Latest awards to bioinfo89

Popular Question 4 months ago, created a question with more than 1,000 views. For How to annotate novel SNPs using coding sequence position?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to extract forward and reverse primer coordinates for soft clipping?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to extract unique paired end reads from a merged BAM file?
Popular Question 6 months ago, created a question with more than 1,000 views. For RUM aligner - perl precedence error
Popular Question 8 months ago, created a question with more than 1,000 views. For How to extract unique paired end reads from a merged BAM file?
Popular Question 8 months ago, created a question with more than 1,000 views. For RUM aligner - perl precedence error
Great Question 14 months ago, created a question with more than 5,000 views. For Merge vcf files with multiple samples into one vcf with all variants
Popular Question 14 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
Popular Question 22 months ago, created a question with more than 1,000 views. For Merge vcf files with multiple samples into one vcf with all variants
Popular Question 22 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
Popular Question 24 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
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Scholar 2.7 years ago, created an answer that has been accepted. For A: How to extract unique paired end reads from a merged BAM file?

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