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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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Where to download baseline microsatellites information file? #29

Closed Nana7926 closed 2 months ago

Nana7926 commented 3 years ago

I notices the notes in the README file said "2. If you don't have normal samples to build baseline(baseline step for tumor only sample detection), you can download the microsatellites information with baseline on our github or use -i option in pro module to set a hard cutoff directly.". May I know the exact link to download the file? Thanks

PengJia6 commented 3 years ago

@Nana7926 Thanks for your question!

We have the baseline files of CRC,STAD and UCEC built by TCGA dataset. But, these baselines are just for GRCh38 aligned bam file. And I will send you by email.

chenzemin commented 1 year ago

@Nana7926 Thanks for your question!

We have the baseline files of CRC,STAD and UCEC built by TCGA dataset. But, these baselines are just for GRCh38 aligned bam file. And I will send you by email.

Could you also send me a copy? Thank you very much.

aaraneo21 commented 1 year ago

@Nana7926 Thanks for your question!

We have the baseline files of CRC,STAD and UCEC built by TCGA dataset. But, these baselines are just for GRCh38 aligned bam file. And I will send you by email.

Could you please send me a copy as well? Thanks so much!

ankurs103 commented 1 year ago

@Nana7926 Thanks for your question!

We have the baseline files of CRC,STAD and UCEC built by TCGA dataset. But, these baselines are just for GRCh38 aligned bam file. And I will send you by email.

Can you please send me a copy/link as well? My Email is : liver.hepato@gmail.com . Thanks in advance

Taoyegbio commented 1 year ago

@Nana7926 Thanks for your question!

We have the baseline files of CRC,STAD and UCEC built by TCGA dataset. But, these baselines are just for GRCh38 aligned bam file. And I will send you by email.

Can you please send me a copy/link as well? My Email is : qqlzt123456@163.com . Thanks so much!

OrangePomeranian commented 5 months ago

Can I also get the link/copy? Email: d.plewa25@gmail.com Thank you very much

PengJia6 commented 2 months ago

@chenzemin @OrangePomeranian @Taoyegbio @ankurs103 @aaraneo21 @Nana7926

Please find the baseline file here: https://github.com/xjtu-omics/msisensor-pro/tree/master/data