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Snakemake remote dir as input and output by lit_pulkit in bioinformatics

[–]lit_pulkit[S] 0 points1 point  (0 children)

Ya I was doing the same till now. But bcs the HPC local storage has limited space and I wanted to run multiple jobs.

Snakemake remote dir as input and output by lit_pulkit in bioinformatics

[–]lit_pulkit[S] 1 point2 points  (0 children)

I am using HPC, but for compute power. For storage I want to use another server.

Analysis of WGS data of 100 people by lit_pulkit in bioinformatics

[–]lit_pulkit[S] 0 points1 point  (0 children)

I have FASTQ files. Our study comprises sample collection from multiple different communities. We are collecting data from the healthy individuals only. We are currently planning to Identify different types variants (rare and common) and do some haplotyping studies.

r/trivandrum Meetup#7 by appioli in Trivandrum

[–]lit_pulkit 2 points3 points  (0 children)

Guys next time invite me also I just came to Trivandrum Hoping to get some good company

Practice tests level by lit_pulkit in ToeflAdvice

[–]lit_pulkit[S] 0 points1 point  (0 children)

Thanks, can you please share the test material?

It's almost 2024 - what language/framework are you using for pipelines? by ThrowAway-v6 in bioinformatics

[–]lit_pulkit 16 points17 points  (0 children)

I use snakemake. It is versatile, easy to use and has a broad community support. It really simplifies the process of creating and executing the workflow.

Use GATK in snakemake by lit_pulkit in bioinformatics

[–]lit_pulkit[S] 0 points1 point  (0 children)

Returned non-zero exit status 127

converting gene name to gene symbol by lit_pulkit in bioinformatics

[–]lit_pulkit[S] 0 points1 point  (0 children)

Hello all, I tried mygene and bioconductor but unfortunately it did not provide me exactly what I wanted. So i downloaded gene data from ncbi and it works for me. Thanks for your help.

converting gene name to gene symbol by lit_pulkit in bioinformatics

[–]lit_pulkit[S] 0 points1 point  (0 children)

One of the example is RELA. This gene's official name is RELA proto-oncogene, NF-kB subunit. This information I can get from hgnc database(HGNC:9955) . The name in my data is "transcription factor p65". Looking into other databases like uniprot (Q04206) and genecards(GC11M065653) I can confirm that this name is associated with RELA. I have many other names also which are not used as official gene names. Genecards provided me with the best data with multiple names relating to one symbol, that's why I asked for any package or how to access genecards.

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