User: paumarc

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

Posts by paumarc

<prev • 22 results • page 1 of 3 • next >
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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 5 weeks 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 9 weeks 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 9 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by paumarc10
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Comment: C: stringtie merge error bam file not sorted
... no spaces at margelist.txt file. ...
written 10 weeks 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 10 weeks ago by paumarc10 • updated 10 weeks ago by finswimmer8.1k
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Comment: A: stringtie merge error bam file not sorted
... Ok, I am sorry, i just forget to paste it the error says : **the input alignment file is not sorted!** the strange thing about the error is that it happens always with the last file (it do not matter if margelist has 2 or 10 bam files), it works normally until it is going to end. It also occurs ...
written 10 weeks ago by paumarc10
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stringtie merge error bam file not sorted
... Hello I am having an error using the following command line: stringtie --merge -p 8 -G /home/ltr2/Genomes/GTF/hg19.gtf -o onwork/hisat2_test/gtf/stringtie_marged.gtf onwork/hisat2_test/margelist.txt bam files has been sorted and indexed with samtools (so they are sorted) and hg19-fasta and h ...
stringtie rna-seq written 10 weeks ago by paumarc10

Latest awards to paumarc

Scholar 9 weeks 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 16 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

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