Microsatellite loci for hg38

[audyavar]

Hello -

I am trying to use MSISensor on WES paired tumor-normal data aligned to hg38. I downloaded the fastq files from UCSC and ran the scan command to generate the list of microsatellite loci for hg38. The program has been stalled for hours. Is this normal? Is there a way to thread/fork this so it does this faster?

msisensor scan -d /mnt/hg38.fa.gz -o /mnt/msisensor_files/microsatellites_hg38.list

[ZhaoDanOnGitHub]

Before using the scan command, you need to decompress the file hg38.fa.gz. You can use "gunzip hg38.fa.gz" to extract the *.gz file and then run the command "msisensor scan -d /mnt/hg38.fa -o /mnt/msisensor_files/microsatellites_hg38.list".

[audyavar]

Thank you! Worked like a charm and only took a few minutes to complete. Is the .bed file required to run msisensor? If so what should the bed file be - tumor or normal or reference genome? Sincerely, Akshata

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On Apr 18, 2019, 7:22 PM -0700, ZhaoDanOnGitHub ***@***.***>, wrote: Before using the scan command, you need to decompress the file hg38.fa.gz. You can use "gunzip hg38.fa.gz" to extract the *.gz file and then run the command "msisensor scan -d /mnt/hg38.fa -o /mnt/msisensor_files/microsatellites_hg38.list". — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[ZhaoDanOnGitHub]

The .bed file is not required. You can specify the area you want to analyze through the .bed file. The .bed file contains 3 columns, which are the chromosome number, start position, end position, gene name. Such as:
1 11867 12229 DDX11L1
1 12611 12723 DDX11L1
1 13219 14411 DDX11L1
There is a example.bed file under the test file, you can refer to it.