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48 Open 52 Closed
48 Open 52 Closed
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Issues list

[BUG] possibly improper MD tag generation whej running atac data. bug Something isn't working
#162 opened May 8, 2024 by LinearParadox
2
Repetitive or low-quality barcode sequences in scATAC data bug Something isn't working
#161 opened Apr 24, 2024 by jeremymsimon
1
[BUG]For HiC data, the size of SAM files outputted using Chromap is much smaller compared to those from BWA-MEM bug Something isn't working
#160 opened Apr 21, 2024 by xujialupaoli
4
[BUG] Support for combinatorial barcode indexing(like SHARE) not present bug Something isn't working
#156 opened Mar 25, 2024 by emattei
3
[BUG] Manpage is down bug Something isn't working
#155 opened Mar 25, 2024 by emattei
1
multi-mapped reads bug Something isn't working
#154 opened Mar 14, 2024 by lindsayhrlee
3
ATAC-seq single end?
#152 opened Mar 11, 2024 by lindsayhrlee
3
[BUG] output to /dev/stdout bug Something isn't working
#150 opened Feb 22, 2024 by lvyunyunSCI
4
how to keep multi-mapped paires for HiC data.
#148 opened Jan 17, 2024 by ming1211
1
Different ValidPairs rate between chromap and bowtie2 in HiC data
#147 opened Jan 9, 2024 by WangZhSi
9
"Number of mapped reads" from log file
#144 opened Nov 28, 2023 by BingjieZhang
3
[BUG] summary and log are confusing. bug Something isn't working
#143 opened Nov 21, 2023 by ming1211
6
An unknown error
#142 opened Nov 14, 2023 by xiadawei123
32
Chromap miss some region when deal with Hetero Chromatin
#141 opened Oct 6, 2023 by ming1211
3
default MAPQ-threshold
#140 opened Aug 31, 2023 by slbai01
1
Error TLEN infomation at hic sam module
#139 opened Aug 31, 2023 by slbai01
3
very low number of mapped read when using --read-format bug Something isn't working
#136 opened Aug 26, 2023 by nouroddinc
15
Assertion `num_minimizers <= static_cast<size_t>(INT_MAX)' failed bug Something isn't working enhancement New feature or request
#131 opened Jan 27, 2023 by minjeongjj
24
compared with Bowtie2.
#130 opened Jan 26, 2023 by ming1211
3
incomplete bed output file generated from Chromap with Chip-seq data
#122 opened Nov 16, 2022 by ming1211
19
Use Cases for Chromap compared to BWA-MEM
#109 opened Sep 8, 2022 by sqhang
1
Pair-end reads?
#106 opened Aug 18, 2022 by lindsayhrlee
6
Output peak by cell count matrix or mtx file
#105 opened Jul 20, 2022 by dbrg77
11
barcode length limit?
#103 opened Jul 18, 2022 by lin-zhongbao
4
Chromap for processing the complex barcodes in two paired reads
#101 opened Jul 13, 2022 by lin-zhongbao
1
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