haowenz / chromap

Fast alignment and preprocessing of chromatin profiles

https://haowenz.github.io/chromap/

haowenz/chromap Issues

why so slow?
Updated a month ago2
Mapping paired-end single-cell ATAC-Seq reads
Closed 2 months ago2
An unknown error
Updated 2 months ago32
[BUG] possibly improper MD tag generation whej running atac data.
Updated 3 months ago2
Repetitive or low-quality barcode sequences in scATAC data
Updated 3 months ago1
[BUG]For HiC data, the size of SAM files outputted using Chromap is much smaller compared to those from BWA-MEM
Updated 3 months ago4
[BUG] chromap map Hi-C short reads Parameters: error threshold
Closed 3 months ago2
[BUG] Support for combinatorial barcode indexing(like SHARE) not present
Updated 4 months ago3
ATAC-seq single end?
Updated 4 months ago3
[BUG] Manpage is down
Updated 4 months ago1
multi-mapped reads
Updated 4 months ago3
Coordinate system of the output fragment file?
Closed 5 months ago1
Understanding the multi-mapping reads and whether they are part of the bed file
Closed 5 months ago2
[BUG] output to /dev/stdout
Updated 5 months ago4
Assertion `num_minimizers <= static_cast<size_t>(INT_MAX)' failed
Updated 6 months ago24
[BUG] summary and log are confusing.
Updated 6 months ago6
how to keep multi-mapped paires for HiC data.
Updated 6 months ago1
Different ValidPairs rate between chromap and bowtie2 in HiC data
Updated 6 months ago9
[Feature Request] report number of duplicated fragments in bulk
Closed 7 months ago4
"Number of mapped reads" from log file
Updated 8 months ago3
Chromap miss some region when deal with Hetero Chromatin
Updated 10 months ago3
Error TLEN infomation at hic sam module
Updated a year ago3
How I can get pairedTagAlign or bedpe output result from bulk ChIP-seq sequencing?
Closed a year ago4
default MAPQ-threshold
Updated a year ago1
very low number of mapped read when using --read-format
Updated a year ago15
[BUG] Segmentation fault (core dumped) HiC
Closed a year ago4
Didn't reach the end of sequence file, which might be corrupted!
Closed a year ago3
Export meta.file like 10x cellranger
Closed a year ago10
barcode length limit?
Updated a year ago4
Question about Hi-C filtering
Closed a year ago1
Numbers of reads and barcodes don't match!
Closed a year ago1
compared with Bowtie2.
Updated 2 years ago3
[BUG] void chromap: :Index: :Load(): Assertion‘ index_ file != nullptr' failed. (Bulk ATAC-seq)
Closed 2 years ago2
SAM output does not include mate-pair information with paired-end reads
Closed 2 years ago3
TLEN column are all 0s
Updated 2 years ago2
Barcode not in translation table
Closed 2 years ago26
[ERROR] barcode length is greater than 32
Closed 2 years ago4
Is there a proper way to generate bigwig file from bed output?
Updated 2 years ago4
Output peak by cell count matrix or mtx file
Updated 2 years ago11
incomplete bed output file generated from Chromap with Chip-seq data
Updated 2 years ago19
Error fragments generated by chromap
Closed 2 years ago4
manpage -1 -2 options
Closed 2 years ago2
Description of log read counts
Closed 2 years ago6
Output both pair and sam files for Hi-C
Closed 2 years ago2
Use Cases for Chromap compared to BWA-MEM
Updated 2 years ago1
Pair-end reads?
Updated 2 years ago6
Chromap for processing the complex barcodes in two paired reads
Updated 2 years ago1
scATAC-seq error: invalid next size (fast)
Closed 2 years ago6
chip pre-set uniquely mapped alignments
Closed 2 years ago1
Output unsorted SAM
Updated 2 years ago3