Dear PIGx ChIP-seq pipeline developers,
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Dr. Bora Uyar
Bioinformatics Scientist
Bioinformatics and Omics Data Science
Max Delbrueck Center (MDC) for Molecular Medicine
The Berlin Institute for Medical Systems Biology (BIMSB):
Hannoversche Str. 28, 10115 Berlin
email: bora...@mdc-berlin.de
mobile: +49 172 949 5680
Thank you very much, I apologise for such a silly mistake. Another (probably) silly question: how do I fix these mistakes? Peaks1 and peaks2 are calculations from two separate studies, each containing several control samples and several input samples.
And also how I can delete whitespaces from the fasta genome file?
On 12. Oct 2022, at 15:45, Elizavet...@mdc-berlin.de wrote:
Thank you for your help. I have run these commands for fasta and gtf files but the error "Genome fasta headers contain whitespaces. Please reformat the headers" persists.Here is what the original headers look like in the fasta file:
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And this is how, after applying formatting:
<pastedImage.png>
Thank you. How long approximately should this line of code take to execute? I've already had it running for 30 minutes.
Lisa
I tested this code:
cat Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa | awk '{ print $1}' > refGenome_noWhiteSpace.fa
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I just waited and it worked :) now I've started the pipeline, so far it's going without errors. Thank you very much for your help!
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Hello, the ChIP-seq Pipeline has an error again (extract_nucleotide_frequency rule), I am sending you an error message (log file for this rule is empty):
On 13. Oct 2022, at 12:37, Elizavet...@mdc-berlin.de wrote:
Hello, the ChIP-seq Pipeline has an error again (extract_nucleotide_frequency rule), I am sending you an error message (log file for this rule is empty):
<pastedImage.png>
Thank you, the problem was indeed related to the required memory.
Best,
Lisa