xjtu-omics msisensor-pro issues

xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

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issues

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failed to open output files to write !

#73 Bang9suK opened 3 weeks ago
0
Output MSIsensor-pro (unstable, dis and all)

#72 OrangePomeranian opened 2 months ago
0
seline files for cancer samples only

#71 20221122 opened 2 months ago
0
Should masked fasta or unmasked fasta be used for scanning?

#70 Weiyifan opened 3 months ago
0
Change OS from Ubuntu 18.04 to 22.04 on Dockerfile

#69 Soupionis-Spiros closed 4 months ago
0
failed to open file: /local/scrath/test/homo.list

#68 songeric1107 opened 5 months ago
0
Does the msi site for a target panel need to be filtered?

#67 h170607 opened 8 months ago
0
Remove microsatellites with CpG context

#66 bounlu opened 8 months ago
0
Matched vs tumor_only scores

#65 bounlu opened 8 months ago
0
Parallelization of samples for baseline

#64 bounlu opened 8 months ago
1
the place to put .bam.bai

#63 Elizabeth237 closed 11 months ago
2
Threshold TCGA

#62 MirandaStobbe opened 1 year ago
1
issues on toy dataset

#61 nservant opened 1 year ago
2
Baseline for tumor only

#60 da-otero opened 1 year ago
5
Baseline for tumor Only

#59 da-otero closed 1 year ago
1
diffrent results by using diffrent homopolymer and microsates files(just diff in microsates size)

#58 ZooJooFoo opened 1 year ago
1
Having issue at Assert(idx) for msi tumor/normal

#57 shivUSF closed 11 months ago
1
How to determine the exact number of repetition of a MSI site in tumor samples

#56 Giuseppe1995 closed 1 year ago
4
Baseline step for tumor-only pipeline

#55 komalsrathi opened 1 year ago
2
Files format page not working

#54 bahreinia closed 1 year ago
2
Scan output

#53 yazbeck closed 1 year ago
1
A few questions about baseline making

#52 RADIOMUMM opened 1 year ago
1
Unable to use CRAM inputs for msisensor-pro

#51 seetarajpara opened 1 year ago
2
How to determine low and high cut-offs?

#50 komalsrathi closed 1 year ago
5
Reference file issue even when providing the correct file

#49 komalsrathi closed 1 year ago
1
Installation and run errors

#48 komalsrathi closed 1 year ago
2
Baseline files

#47 ericbio closed 1 year ago
1
bam file error when running "msisensor-pro baseline" step

#46 YXbioinfor opened 1 year ago
2
The MSI loci both in output.prefix_germline and output.prefix_somatic

#45 litun-fkby opened 2 years ago
2
Minimum homopolymer length (msisensor-pro baseline is killed if it is set to 5)

#44 emesexochitl opened 2 years ago
2
Could it run on msisensor-pro that using different type of data between the 2nd step ( build baseline ) and the 3rd step ( evaluate MSI )

#43 bio-rain opened 2 years ago
2
MSISensor normalization issue. Please help!

#42 seifudd opened 2 years ago
1
Less than 200% cpu usage even set -b to 10

#41 xzhub closed 2 years ago
2
No MSI found

#40 davidlord closed 1 year ago
7
Index not found with symlinked files

#39 fbdtemme opened 2 years ago
1
msisensor scan segfault

#38 b-math closed 2 years ago
2
How to classify the MSI high and MSI low ?

#37 wangxiaoshine opened 2 years ago
1
Cannot open configure file in msisensor-pro 1.2.0

#36 Dichromatism opened 2 years ago
3
feature request: indicate deletion or insertions

#35 kcleal closed 2 years ago
3
conda install failed

#34 wqrao opened 2 years ago
1
conda install failed

#33 wqrao closed 2 years ago
0
discriminative microsatellite site (DMS) from paper

#32 syan1 opened 2 years ago
4
Support cram files

#31 kcleal closed 2 years ago
4
htslib error using the precompiled binary

#30 kcleal closed 2 years ago
1
Where to download baseline microsatellites information file?

#29 Nana7926 opened 2 years ago
6
Segmentation fault (core dumped)

#28 iichelhadi closed 2 years ago
12
pro scan context_length = 9 failed, shorter `-c` induces systematic errors

#27 ruolin opened 3 years ago
4
exclude secondary alignment and have mapq cutoff

#26 ruolin opened 3 years ago
4
Program aborted:Same reference genome file should be used in both 'scan' and msi/pro/baseline steps

#25 Zho-o-o-u closed 3 years ago
5
fatal error: failed to open ref file

#24 lancermiss closed 3 years ago
4