User: ciemanek

gravatar for ciemanek
ciemanek140
Reputation:
140
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Location:
The Netherlands/Amsterdam
Last seen:
11 months, 3 weeks ago
Joined:
4 years, 3 months ago
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Posts by ciemanek

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Samtools fastq returns less unmapped than flagstat
... Yes - the problem was the dummy data I was generating, the reads headers specifically - it seems that for R1/R2 reads this information was getting lost in BAM file while sorting by name and as a result, twice fewer reads were returned. ...
written 12 months ago by ciemanek140
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Comment: C: Samtools fastq returns less unmapped than flagstat
... Removing sed from the pipeline doesn't change the outcome - only when I remove `-n` argument from `samtools sort` I get the number of reads I'm supposed to according to `samtools flagstat` ...
written 12 months ago by ciemanek140
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Comment: C: Samtools fastq returns less unmapped than flagstat
... I also tried this approach on paired-end data with appropriate flags (`samtools fastq -f 13 -T ZI --threads 4 -1 output_filtered_R1.fq -2 output_filtered_R2.fq`) and it returns exactly the number of reads it should. ...
written 12 months ago by ciemanek140
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Comment: C: Samtools fastq returns less unmapped than flagstat
... Did you also run sorting by name? Apparently, when I run the command without `-n` option for `samtools sort`, I get all the reads I should get. ...
written 12 months ago by ciemanek140
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Comment: C: Samtools fastq returns less unmapped than flagstat
... Thanks :) I just grepped my filtered fastq for the header (@plasmid) and checked number of printed lines with `wc -l`, which returned 2500 read headers (which makes sense since output file is 10 000 lines, considering a single read being represented by 4 lines in fastq). ...
written 12 months ago by ciemanek140
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Samtools fastq returns less unmapped than flagstat
... I am trying to include filtering reads in my pipeline. I do this by aligning the reads to a reference sequence with `bwa mem` (afterwards I run modifying headers with `sed` and sorting reads by name with `samtools sort -n` as advised by `samtools` manual) and outputting the reads that didn't map wit ...
ngs alignment samtools filtering written 12 months ago by ciemanek140 • updated 12 months ago by Biostar ♦♦ 20
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Comment: C: Filtering human reads in metagenomics: should supplementary reads be removed?
... thanks a lot for the answer :) ...
written 14 months ago by ciemanek140
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Comment: C: Filtering human reads in metagenomics: should supplementary reads be removed?
... What I mean are reads mapped by bwa mem as supplementary - they are listed with samtools flagstat as below: 4086053 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 482807 + 0 supplementary 0 + 0 duplicates 964819 + 0 mapped (23.61% : N/A) 0 + 0 paired in seq ...
written 14 months ago by ciemanek140
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Filtering human reads in metagenomics: should supplementary reads be removed?
... I want to filter out human 'contaminants' from my metagenomic sample. I mapped my reads to a human genome and I am filtering them with samtools. So far, I only filter out reads that had mapping flag, but should I also add a flag for removing supplementary reads while filtering? I can't wrap my head ...
flagstat metagenomics dna-seq samtools bwa written 14 months ago by ciemanek140
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Comment: C: How to acknowledge in the paper a reference genome that hasn't been published ye
... There is no paper regarding this particular genome and it is not available for download to the best of my knowledge. It was assembled by people I collaborate with, but as far as I understood their idea is to publish it in another paper in some time. The only information I have is that it was assembl ...
written 2.1 years ago by ciemanek140

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