Comments (3)
For these files that only need to scan once, would command like
./chromap ... --barcode-whitelist <(zcat whitelist.tsv.gz) work on your platform?
from chromap.
Hi @mourisl , yes, it works. However, we are building workflows, which means we do not have control of what white list people will provide (either gzipped or not). We can take care of it at the workflow level (i.e. test if suffix is 'gz' and if so, gunzip). But I think it is more elegant if chromap can take care of this step because for FASTQ files, you already have support for both .fq and .fq.gz.
from chromap.
Sorry for the delayed replay after almost one year, which I totally forgot to work on until another recent issue. We just added the feature to directly support gzipped whitelist file #127 . If your team is still interested in this feature, could you please give it a try?
from chromap.
Related Issues (20)
- "Number of mapped reads" from log file HOT 3
- [Feature Request] report number of duplicated fragments in bulk HOT 4
- Different ValidPairs rate between chromap and bowtie2 in HiC data HOT 9
- how to keep multi-mapped paires for HiC data. HOT 1
- [BUG] output to /dev/stdout HOT 6
- Understanding the multi-mapping reads and whether they are part of the bed file HOT 2
- ATAC-seq single end? HOT 3
- Coordinate system of the output fragment file? HOT 1
- multi-mapped reads HOT 3
- [BUG] Manpage is down HOT 1
- [BUG] Support for combinatorial barcode indexing(like SHARE) not present HOT 3
- [BUG] chromap map Hi-C short reads Parameters: error threshold HOT 2
- [BUG]For HiC data, the size of SAM files outputted using Chromap is much smaller compared to those from BWA-MEM HOT 4
- Repetitive or low-quality barcode sequences in scATAC data HOT 1
- [BUG] possibly improper MD tag generation whej running atac data. HOT 3
- Mapping paired-end single-cell ATAC-Seq reads HOT 2
- why so slow? HOT 2
- Failure to load cellular barcodes containing Ns HOT 3
- Understanding the terminologies from stderr and summary HOT 11
- possible issue with /dev/stdout redirection HOT 2
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from chromap.