haowenz chromap issues - Githubissues

haowenz / chromap

Fast alignment and preprocessing of chromatin profiles

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

MIT License

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issues

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[BUG] tabix error [E::hts_idx_push]chromosome blocks not continuous

#172 lishuangshuang0616 closed 3 weeks ago
3
Segmentation fault

#171 lunky-zao opened 3 weeks ago
1
Assertion `mapping_output_file_ != __null' failed

#170 lunky-zao opened 1 month ago
1
possible issue with /dev/stdout redirection

#169 Overcraft90 closed 1 month ago
2
Semi-adaptively increase temp file size. Count whitelist-only barcode in summary.

#168 mourisl closed 1 month ago
0
Understanding the terminologies from stderr and summary

#167 dbrg77 closed 1 month ago
11
Failure to load cellular barcodes containing Ns

#166 ste-depo closed 2 months ago
3
why so slow?

#165 zhaotao1987 closed 2 months ago
2
Mapping paired-end single-cell ATAC-Seq reads

#164 NPSDC closed 4 months ago
2
Generate temporary files at local directory if output is set to stdout

#163 mourisl closed 4 months ago
0
[BUG] possibly improper MD tag generation whej running atac data.

#162 LinearParadox opened 4 months ago
3
Repetitive or low-quality barcode sequences in scATAC data

#161 jeremymsimon opened 5 months ago
1
[BUG]For HiC data, the size of SAM files outputted using Chromap is much smaller compared to those from BWA-MEM

#160 xujialupaoli closed 2 months ago
4
[BUG] chromap map Hi-C short reads Parameters: error threshold

#159 Hanjiangna closed 5 months ago
2
Generate temporary files at local directory if output is set to stdout

#158 mourisl closed 4 months ago
1
Update manpage link in README.md

#157 swiftgenomics closed 6 months ago
0
[BUG] Support for combinatorial barcode indexing(like SHARE) not present

#156 emattei opened 6 months ago
3
[BUG] Manpage is down

#155 emattei opened 6 months ago
1
multi-mapped reads

#154 lindsayhrlee opened 6 months ago
3
Coordinate system of the output fragment file?

#153 JiaxinLi-lipluszn closed 6 months ago
1
ATAC-seq single end?

#152 lindsayhrlee opened 6 months ago
3
Understanding the multi-mapping reads and whether they are part of the bed file

#151 NPSDC closed 6 months ago
2
[BUG] output to /dev/stdout

#150 lvyunyunSCI opened 7 months ago
6
Fix a bug in the summary file for SAM format output. Add the duplicate count in the bulk data BED output.

#149 mourisl closed 8 months ago
0
how to keep multi-mapped paires for HiC data.

#148 ming1211 opened 8 months ago
1
Different ValidPairs rate between chromap and bowtie2 in HiC data

#147 WangZhSi opened 8 months ago
9
Move li_dev4's content to li_dev5, including no-sorting read-format, …

#146 mourisl closed 9 months ago
0
[Feature Request] report number of duplicated fragments in bulk

#145 dawe closed 9 months ago
4
"Number of mapped reads" from log file

#144 BingjieZhang opened 10 months ago
3
[BUG] summary and log are confusing.

#143 ming1211 opened 10 months ago
6
An unknown error

#142 xiadawei123 opened 10 months ago
34
Chromap miss some region when deal with Hetero Chromatin

#141 ming1211 opened 11 months ago
3
default MAPQ-threshold

#140 slbai01 opened 1 year ago
1
Error TLEN infomation at hic sam module

#139 slbai01 opened 1 year ago
3
How I can get pairedTagAlign or bedpe output result from bulk ChIP-seq sequencing?

#138 ezioljj closed 1 year ago
4
Support globbing in read file names

#137 swiftgenomics closed 1 year ago
0
very low number of mapped read when using --read-format

#136 nouroddinc opened 1 year ago
15
[BUG] Segmentation fault (core dumped) HiC

#135 ericmalekos closed 1 year ago
4
Didn't reach the end of sequence file, which might be corrupted!

#134 MonsterLaplace closed 1 year ago
3
Output mapping statistics summary at bulk or barcode-level

#133 mourisl closed 1 year ago
0
Numbers of reads and barcodes don't match!

#132 taotaoyuan closed 1 year ago
1
Assertion `num_minimizers <= static_cast<size_t>(INT_MAX)' failed

#131 minjeongjj opened 1 year ago
24
compared with Bowtie2.

#130 ming1211 opened 1 year ago
3
[BUG] void chromap: :Index: :Load(): Assertion‘ index_ file != nullptr' failed. (Bulk ATAC-seq)

#129 ezioljj closed 1 year ago
2
Add mate information (mate pair coordinate, tlen) to the sam output

#128 mourisl closed 1 year ago
4
Allow gzipped barcode whitelist file.

#127 mourisl closed 1 year ago
5
Update issue templates

#126 haowenz closed 1 year ago
0
[ERROR] barcode length is greater than 32

#125 rargelaguet closed 1 year ago
4
SAM output does not include mate-pair information with paired-end reads

#124 heruiyang closed 1 year ago
3
Refactor SequenceBatch.

#123 swiftgenomics closed 1 year ago
0