User: paumarc

gravatar for paumarc
paumarc10
Reputation:
10
Status:
New User
Location:
Barcelona (ICO)
Last seen:
2 weeks, 3 days ago
Joined:
3 years, 11 months ago
Email:
p******@gmail.com

Posts by paumarc

<prev • 24 results • page 1 of 3 • next >
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Comment: C: find position of 3' utr at entrez
... Can you tell me any example of how to get or tutorial them? it is driving me mad thanks ...
written 17 days ago by paumarc10
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find position of 3' utr at entrez
... Hi I am using the BIOPYTHON library Bio to retrieve sequences from Entrez, I need to know the ending position of 5' UTR and the starting position of 3' UTR. How do I get them? thank you p ...
sequence entrez biopython written 17 days ago by paumarc10
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Same pipeline for exome seq variant calling with different results
... Hello we have been running a pipeline using fastp, bwa-mem, and gatk with hard filtering to perform snp calling on exome seq data. Although the coverage statistics for fastq files is similar, we obtain a huge difference in the number of reads per snp. We wonder if it could be caused by hard filt ...
bwa-mem fastp snp gatk written 10 months ago by paumarc10
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Answer: A: stringtie merge error bam file not sorted
... **Solved:** margelist.txt should have the path of **gtf** files generated by stringtie in the previous step of the pipeline, not the path of bam files ...
written 11 months ago by paumarc10
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Comment: A: how to combine RNA seq data from 4 lanes
... Aling the four fastq separately and marge the bam files with samtools merge ...
written 11 months ago by paumarc10
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Comment: C: stringtie merge error bam file not sorted
... ok, thank you. i was becoming crazy with the output ...
written 11 months ago by paumarc10
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Comment: C: stringtie merge error bam file not sorted
... i post it separatly by mistake, but you can see the margelist.txt ...
written 11 months ago by paumarc10
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Comment: A: stringtie merge error bam file not sorted
... Yes, of course. Notice that at the original file there not exist a blank line between lines with the path. I don't know why (maybe because I am in Linux), when I copy paste, the post at the forum does not recognize the 'new line' /home/ltr2/onwork/hisat2_test/bam/2008-7981.sorted.bam /home/ ...
written 11 months ago by paumarc10
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Comment: C: stringtie merge error bam file not sorted
... no spaces at margelist.txt file. ...
written 11 months ago by paumarc10
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Comment: C: stringtie merge error bam file not sorted
... Thank you for your replay, as i told you all files are sorted properly, and do not mather if i use two or more files at the marge list, it always gives the error at the last bam file /hisat2_test/bam $ ls |xargs -i samtools view -H {} | grep "HD" @HD VN:1.0 SO:coordinate @HD VN: ...
written 11 months ago by paumarc10 • updated 11 months ago by finswimmer12k

Latest awards to paumarc

Popular Question 10 months ago, created a question with more than 1,000 views. For convert CSQ and ANN fields to a tab delimitet document with its headers
Popular Question 10 months ago, created a question with more than 1,000 views. For find snp depth and total depth
Scholar 11 months ago, created an answer that has been accepted. For A: how to retrive the most recent entry from uscs databese to build a bed file
Scholar 2.2 years ago, created an answer that has been accepted. For A: how to retrive the most recent entry from uscs databese to build a bed file

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