User: abedkurdi10
abedkurdi10 • 20
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Posts by abedkurdi10
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... **bedtools maskfasta** requires FASTA as input file. To mask regions in that FASTA file, **bedtools maskfasta** accepts **BED, GFF and VCF** files **as regions to be masked**. So **SNPs in a VCF** file will be masked in the FASTA file.
Also the tool is easy to use:
bedtools maskfasta -fi input.fast ...
written 9 months ago by
abedkurdi10 • 20
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... **bedtools maskfasta** is already available, why writing a script from scratch? ...
written 9 months ago by
abedkurdi10 • 20
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... I think you can use **bedtools maskfasta**, it will do the job. ...
written 9 months ago by
abedkurdi10 • 20
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... Really? Is that an answer?
What I meant is how exactly I can apply it, which tools to use, any starting point! ...
written 11 months ago by
abedkurdi10 • 20
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... Thanks for the fast reply.
Actually, we are looking for germline variants. So, basically, it boils down to the effect size in this case. For this, our biostatistician is going to help.
However, I am curious to know, and maybe other readers of this post, on what would be the case if we are looking ...
written 3.1 years ago by
abedkurdi10 • 20
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... Indeed, it is about power calculation. I need to identify (known and de-novo) mutations for low penetrance genes in cancer patients using panel sequencing of 30 to 50 genes maximum.
Assuming we can achieve an average coverage of 100x, we were wondering if there is a formula/rule that we can use to ...
written 3.1 years ago by
abedkurdi10 • 20
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... No, I am not looking for a specific variant. ...
written 3.1 years ago by
abedkurdi10 • 20
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... Hello all,
I need to know if there is a way to estimate the minimum/optimal **number of samples** needed to detect a variant from panel sequencing (exome sequencing of a set of genes).
I appreciate your help,
thank you.
...
written 3.1 years ago by
abedkurdi10 • 20
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... Hello all,
I wrote an R script, when I run it inside R (using source('/path/to/file.R') it works well. When I run it using Rscript from command line, it throws the following error:
Error in ha_pct + ht : non-numeric argument to binary operator
Calls: oncoPrint
Execution halted
Does any ...
written 3.1 years ago by
abedkurdi10 • 20
• updated
3.1 years ago by
Alex Reynolds ♦ 29k
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... Well, I am running some exome sequencing analysis on one PC, 8 cores and 32GB of RAM. I did some research and found that we can cluster some PCs so we can use their resources (CPU, RAM, hard disk) to speed up my analysis, or even running many analysis in the same time. ...
written 3.1 years ago by
abedkurdi10 • 20
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For raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
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For Thresholds to filter out variants from vcf file
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For VCF file re-header
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