xjtu-omics/msisensor-pro

Issues

• Minimum homopolymer length (msisensor-pro baseline is killed if it is set to 5)

  #44 opened 3 months ago by emesexochitl
  2

• The MSI loci both in output.prefix_germline and output.prefix_somatic

  #45 opened 3 months ago by litun-fkby
  2

• bam file error when running "msisensor-pro baseline" step

  #46 opened 3 months ago by YXbioinfor
  2

• A few questions about baseline making

  #52 opened 3 months ago by RADIOMUMM
  1

• 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 opened 3 months ago by bio-rain
  2

• Baseline step for tumor-only pipeline

  #55 opened 3 months ago by komalsrathi
  2

• How to classify the MSI high and MSI low ?

  #37 opened 3 months ago by wangxiaoshine
  1

• MSISensor normalization issue. Please help!

  #42 opened 3 months ago by seifudd
  1

• Index not found with symlinked files

  #39 opened 3 months ago by fbdtemme
  1

• conda install failed

  #34 opened 3 months ago by wqrao
  1

• Cannot open configure file in msisensor-pro 1.2.0

  #36 opened 3 months ago by Dichromatism
  3

• pro scan context_length = 9 failed, shorter `-c` induces systematic errors

  #27 opened 3 months ago by ruolin
  4

• exclude secondary alignment and have mapq cutoff

  #26 opened 3 months ago by ruolin
  4

• docker image has error while loading libraries

  #23 opened 3 months ago by anoronh4
  8

• diffrent results by using diffrent homopolymer and microsates files(just diff in microsates size)

  #58 opened 3 months ago by ZooJooFoo
  1

• Baseline for tumor only

  #60 opened 3 months ago by da-otero
  5

• issues on toy dataset

  #61 opened 3 months ago by nservant
  3

• Threshold TCGA

  #62 opened 3 months ago by MirandaStobbe
  1

• Parallelization of samples for baseline

  #64 opened 3 months ago by bounlu
  3

• Matched vs tumor_only scores

  #65 opened 3 months ago by bounlu
  1

• Remove microsatellites with CpG context

  #66 opened 3 months ago by bounlu
  1

• Does the msi site for a target panel need to be filtered?

  #67 opened 3 months ago by h170607
  1

• failed to open file: /local/scrath/test/homo.list

  #68 opened 3 months ago by songeric1107
  1

• Should masked fasta or unmasked fasta be used for scanning?

  #70 opened 3 months ago by Weiyifan
  1

• failed to open output files to write !

  #73 opened 3 months ago by Bang9suK
  3

• Output MSIsensor-pro (unstable, dis and all)

  #72 opened 3 months ago by OrangePomeranian
  1

• No MSI found

  #40 opened 2 years ago by davidlord
  8

• Unable to use CRAM inputs for msisensor-pro

  #51 opened 6 months ago by seetarajpara
  2

• Where to download baseline microsatellites information file?

  #29 opened 6 months ago by Nana7926
  7

• discriminative microsatellite site (DMS) from paper

  #32 opened 6 months ago by syan1
  6

• seline files for cancer samples only

  #71 opened 6 months ago by 20221122
  1

• Having issue at Assert(idx) for msi tumor/normal

  #57 opened a year ago by shivUSF
  1

• the place to put .bam.bai

  #63 opened a year ago by Elizabeth237
  2

• Scan output

  #53 opened 2 years ago by yazbeck
  1

• fatal error: failed to open ref file

  #24 opened 4 years ago by lancermiss
  4

• Baseline for tumor Only

  #59 opened 2 years ago by da-otero
  1

• How to determine the exact number of repetition of a MSI site in tumor samples

  #56 opened 2 years ago by Giuseppe1995
  4

• Files format page not working

  #54 opened 2 years ago by bahreinia
  2

• How to determine low and high cut-offs?

  #50 opened 2 years ago by komalsrathi
  5

• Reference file issue even when providing the correct file

  #49 opened 2 years ago by komalsrathi
  1

• Baseline files

  #47 opened 2 years ago by ericbio
  1

• Installation and run errors

  #48 opened 2 years ago by komalsrathi
  2

• msisensor scan segfault

  #38 opened 3 years ago by b-math
  2

• Less than 200% cpu usage even set -b to 10

  #41 opened 3 years ago by xzhub
  2

• feature request: indicate deletion or insertions

  #35 opened 3 years ago by kcleal
  3

• conda install failed

  #33 opened 3 years ago by wqrao
  0

• Support cram files

  #31 opened 3 years ago by kcleal
  4

• htslib error using the precompiled binary

  #30 opened 3 years ago by kcleal
  1

• Segmentation fault (core dumped)

  #28 opened 3 years ago by iichelhadi
  12

• Program aborted:Same reference genome file should be used in both 'scan' and msi/pro/baseline steps

  #25 opened 4 years ago by Zho-o-o-u
  5