1. 30 Oct, 2019 1 commit
  2. 28 Oct, 2019 2 commits
  3. 14 Oct, 2019 1 commit
  4. 16 Apr, 2019 1 commit
  5. 05 Oct, 2018 1 commit
  6. 04 Oct, 2018 1 commit
  7. 22 Jun, 2018 1 commit
  8. 14 Jun, 2018 1 commit
  9. 13 Jun, 2018 1 commit
    • Blaise Li's avatar
      Fix comma typo in input function (ValueError). · a101b0ce
      Blaise Li authored
      The ValueError was:
      `Invalid file path or buffer object type: <class 'snakemake.io.Namedlist'>`
      
      This was due to an extra comma at the end of the return of `source_norm_file`.
      a101b0ce
  10. 08 Jun, 2018 2 commits
  11. 04 Jun, 2018 1 commit
  12. 01 Jun, 2018 1 commit
    • Blaise Li's avatar
      Remapping unmapped reads for iCLIP. · 00f001de
      Blaise Li authored
      The remapping is done with one mismatch allowed in the seed. It happened
      that very little mapped reads had mismatches, although read-through
      reads can have some.
      00f001de
  13. 11 Apr, 2018 1 commit
  14. 08 Mar, 2018 1 commit
  15. 05 Mar, 2018 1 commit
  16. 21 Feb, 2018 1 commit
  17. 16 Feb, 2018 1 commit
  18. 02 Feb, 2018 1 commit
    • Blaise Li's avatar
      Pipeline to process iCLIP data. · 53909846
      Blaise Li authored
      Currently goes from demultiplexing to mapping, via trimming and
      deduplicating. The mapping is performed on 3 read type:
      - adapt_nodedup (the adaptor was found, and the reads were trimmed but
        not deduplicated)
      - adapt_deduped (the adaptor was found, and the reads were trimmed and
        deduplicated)
      - noadapt_deduped (the adaptor was not found, and the reads were trimmed
        and deduplicated)
      
      The trim_and_dedup script currenly assumes that two low-diversity zones
      are present, and ignores them for deduplication:
      
      NNNNNGCACTANNNWWW[YYYY]NNNN
      1---5 : 5' UMI
           6--11: barcode (lower diversity)
                12-14: UMI
                  15-17: AT(or GC?)-rich (low diversity)
                      [fragment]
                             -4 -> -1: 3' UMI
      
      It may be a problem to deduplicate taking into account the end of the
      reads, which tends to be of lower quality. The reads with errors will be
      over-represented. That is why we decided to also look at the
      non-deduplicated reads.
      53909846