User: bioinfo89

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bioinfo8940
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Posts by bioinfo89

<prev • 74 results • page 1 of 8 • next >
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Comment: C: Chia-pipe cannot find the module pigz
... Yes I resolved it. Thanks! ...
written 4 weeks 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 weeks 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 weeks 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 weeks 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 weeks 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 weeks ago by bioinfo8940
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Chia-pipe cannot find the module pigz
... Hi All, I am using Chia-pipe to run chia-pet (cell line) data. I followed the installation process and modified the config file to run the tool. All the modules **(pigz,perl,java,samtools,bedtools)** are also installed in the chia-pipe folder. However, the program terminates with the following erro ...
chia-pet next-gen chip-seq written 4 weeks ago by bioinfo8940 • updated 4 weeks ago by RamRS30k
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What information does ChIA-PET2 tool trim statistics terms provide exactly?
... Hi All, I am analysing ChIA-PET data using ChIA-PET2 tool. I wanted to know what exactly the following terms mean from the trim statistics the tool provides: Expect PETs Expect both PETs 1Empty PETs 2Empty PETs Valid PETs What is the difference between Expected and Expected bo ...
chip-seq written 5 months ago by bioinfo8940 • updated 4 months ago by lakhujanivijay5.3k
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ChIA-PET2: Error: Don't have enough confident interactions to learn the model.
... Hi All, I am currently getting the following error when I use ChIA-PET2: Running MICC... Intra data: ChIAPET_rawdata/rep1_ChIAPET.interactions.intra.bedpe Inter data: ChIAPET_rawdata/rep1_ChIAPET.interactions.inter.bedpe Output file: ChIAPET_rawdata/rep1_ChIAPET.interactions.M ...
chip-seq written 6 months ago by bioinfo8940 • updated 5 months ago by lakhujanivijay5.3k
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Comment: C: bedtools complement error
... Hi @Alex Reynolds, I was just exploring the bedpos `--complement` option instead of bedtools complement option to get coordinates which are present in `genome.bed` but not in `target.bed`, I found `--difference` is more suitable to get the `result.bed`, instead of `--complement`. Do correct me if ...
written 16 months ago by bioinfo8940 • updated 16 months ago by RamRS30k

Latest awards to bioinfo89

Popular Question 3 months ago, created a question with more than 1,000 views. For RUM aligner - perl precedence error
Popular Question 5 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 5 months ago, created a question with more than 1,000 views. For RUM aligner - perl precedence error
Great Question 11 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 11 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
Popular Question 18 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 19 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
Popular Question 21 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
Supporter 23 months ago, voted at least 25 times.
Scholar 2.5 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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