User: A

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Posts by A

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What does they mean by exome size here
... Hi I want to `predict micrpsattelite instability by MSIpred` software which in a part of code needs exome size like tagged_snvs_maf.make_feature_table(exome_size=44) You see for `TCGA` data they put `44` here I have `whole genome sequencing` is exome size here means `captured size of geno ...
wgs wes written 5 weeks ago by A3.9k
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Comment: C: WES or WGS
... I have already WGS, I noticed people done the same project on the same cancer by WES so I am trying to explain why we are repeating such a project by taking any advantage of WGS over the WES into account. In the other way I am justifying why we are doing this project and I can not find a good reason ...
written 6 weeks ago by A3.9k
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Comment: C: WES or WGS
... Thank you. In the cancer I am working on, there is a published list of driver genes already on which I have focused my analysis; In this case, as cancer driver genes are mainly are in the coding regions, so basically I am not beneficial from WGS advantages here because I am focusing on these genes. ...
written 6 weeks ago by A3.9k
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WES or WGS
... Hi If you have human samples of responders to a drug (n=27) and non-responders to this drug (n=38) And have enough money to perform ***whole genome sequencing with depth of 50x coverage for tumours and 30x coverage for normal samples, with 94% of the known genome being sequenced to at least 8× cov ...
exome genome ngs written 6 weeks ago by A3.9k • updated 5 weeks ago by d-cameron2.2k
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Comment: C: GISTIC 2.0 for sequencing data
... By the way I had already asked this question here and got answer https://www.biostars.org/p/377888/ ...
written 6 weeks ago by A3.9k
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Comment: C: GISTIC 2.0 for sequencing data
... I told you I have a script to do that You called copy number with which software? ...
written 6 weeks ago by A3.9k
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Comment: C: GISTIC 2.0 for sequencing data
... No it is not required I have tried that ...
written 6 weeks ago by A3.9k
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Comment: C: GISTIC 2.0 for sequencing data
... Gistic2 works without marker file I have a script calculating the marker file if you want ...
written 6 weeks ago by A3.9k
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Comment: C: visualizing mutational data using Maftools for reference genome hg19
... Actually you don't need this I suggest you may just download maf file for cancer of your interest here ![enter image description here][1] [1]: https://i.ibb.co/RYkcfbF/Screenshot-2020-09-07-at-09-53-19.png You then use `merge_maf` function from Maftools itself to read what you have downloade ...
written 6 weeks ago by A3.9k
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Comment: C: Installing qgraph package on Mac
... Thank you I have not tried that yet I would let you know soon ...
written 6 weeks ago by A3.9k

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