msisensor-pro

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

2

when use msisensor or msisensor-pro msi to analyze the tumor-normal pair data , some MSI loci both in output.prefix_germline and output.prefix_somatic，such as: CRC_16_germline chr1 151196702 GATTG 9 T CCCCC 9|9...

litun-fkby

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

2

When I do the scanning on my genome (Hg19) and I set the minimum length of the homopolymer markers to 5, it finishes, but when I try to generate the...

emesexochitl

MSISensor normalization issue. Please help!

1

Hi, We are running MSISensor version 0.60 for some clinical trials using whole exome sequencing (WES) data. We are using deduplicated BAM files as input. All other parameters set to...

seifudd

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

2

Dear author ： i got a very strange error when i runing ` msisensor-pro baseline -d $ref_list/reference.list -i configure.txt -o ./ ` **Open bam file failed( ), please provide valid...

YXbioinfor

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

2

I have some normal sample sequence data (WGS), and some tumor sequence data (WES/WXS). I'd like to use normal data (WGS) to build baseline, then use tumor data to evaluate...

bio-rain

more documentation on what the outputs mean?

4

Hello, Can you guys provide a bit more info on what the outputs from the `msisensor-pro msi` results mean? I see there are the _prefix_, _dis, _germline, __somatic files. It...

boyangzhao

docker image has error while loading libraries

8

I am trying to run msisensor using the dockerhub image `pengjia1110/msisensor-pro:latest`. i am running with singularity v 3.3.0 and getting the following error: ``` $ singularity exec ./msisensor-pro_latest.sif msisensor-pro msisensor-pro:...

anoronh4

How to classify the MSI high and MSI low ?

1

How to classify the MSI high and MSI low ? Looking forward to your reply.

wangxiaoshine

Index not found with symlinked files

1

I have a directory with a cram and cram index file which are both symlinks. ``` 9876T.recal.crai -> /home/fbdtemme/Documents/sarek/work/stage/32/6f1c18/9876T.recal.cram.crai 9876T.recal.cram -> /home/fbdtemme/Documents/sarek/work/stage/2f/682545/9876T.recal.cram ``` When running msisensor-pro baseline in that directory...

fbdtemme

Cannot open configure file in msisensor-pro 1.2.0

3

Hi, I have tried msisensor-pro (both installed by conda and pulled from docker). When I was using hg19 as a reference and tried to make a baseline using my .bam...

Dichromatism