Discussions

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  🙏

  Can I filter pairs on --max-insert-size, --max-inter-align-gap and --max-molecule-size downstream of parsing?

  bskubi asked Mar 19, 2024 in Q&A · Answered

  

  

  

  

  4
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  🙏

  pairtools parse, dedup and sort use only a few cores per process

  jiangshan529 asked Oct 24, 2023 in Q&A · Unanswered

  

  

  

  

  6
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  🙏

  Large datasets: can I use CRAM and BAM as input? Can I compress the .pairs output?

  amvarani asked Jan 24, 2024 in Q&A · Unanswered

  

  

  

  

  5
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  💡

  binary file format for pairs

  enhancement

  golobor started Sep 29, 2020 in Ideas

  

  

  8
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  🙏

  How to convert .pairs to .tsv

  kayarimagenomics asked Jan 17, 2024 in Q&A · Unanswered

  

  

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  🙏

  Pairtools installation fault. Need help.

  Khewahah asked Jan 11, 2024 in Q&A · Unanswered

  

  

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  🙌

  Why do strands of pairs generated by pairtools parse differ from those in .sam alignments

  jiangshan529 started Jan 20, 2023 in Show and tell

  

  

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  💡

  Estimating Hi-C library resolution

  aminakur started Nov 23, 2022 in Ideas

  

  

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  📣

  v1.0.2

  agalitsyna announced Nov 8, 2022 in Announcements

  

  

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  🙏

  ImportError: cannot import name 'dedup_cython' from partially initialized module 'pairtools.lib'

  georgette-femerling asked Sep 27, 2022 in Q&A · Unanswered

  

  

  

  

  18
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  🙏

  Resolving python import loop error?

  vickietr asked Aug 29, 2022 in Q&A · Answered

  

  

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  💡

  pairtools v1.0.0 roadmap

  agalitsyna started Apr 6, 2022 in Ideas

  

  

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  📣

  v1.0.0

  agalitsyna announced Aug 24, 2022 in Announcements

  

  

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  💡

  Report insertions/deletions in reads

  agalitsyna started Jul 14, 2022 in Ideas

  

  

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  💡

  CLI to add header

  Phlya started Apr 8, 2022 in Ideas

  

  

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  🙏

  high percentage of **total_single_sided_mapped**

  help wanted

  wbszhu asked Apr 12, 2022 in Q&A · Unanswered

  

  

  

  

  9
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  💬

  should we store stats as YAML (or json)

  enhancement question

  sergpolly started Jan 31, 2020 in General

  

  

  

  

  4
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  💬

  improve distance binning for FR,RR,FR,RF pairs "scalings" in stats output

  enhancement

  sergpolly started Feb 21, 2020 in General

  

  

  

  

  11
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  💡

  calculate Pc(s) in stats

  enhancement

  golobor started Nov 28, 2017 in Ideas

  

  

  

  

  4
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  💡

  make auto_open default to stdin/stdout when path evaluates to False

  golobor started Sep 6, 2017 in Ideas

  

  

  1
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  💬

  in all pairsamtools, have a unified way to provide/override column indices and the separator

  golobor started Sep 8, 2017 in General

  

  

  1
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  💬

  PairTools sort failure on merged data

  dowenlab started May 26, 2020 in General

  

  

  

  

  9
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  💬

  pairsamtools subsampling [new tool, enhancement]

  sergpolly started May 15, 2018 in General

  

  

  

  

  5
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  📣

  speedup Hi-C analysis with bwa mem2

  enhancement

  agalitsyna announced Apr 7, 2022 in Announcements

  

  

  0
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  💬

  standalone flip fails when "reduced.chrom.sizes" provided, should go lexicographical

  enhancement

  sergpolly started Jan 25, 2021 in General

  

  

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