User: sangram_keshari

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sangram_ksahu
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Bioinformatics Student, Working in the field of Computational Genomics.

Posts by sangram_keshari

<prev • 48 results • page 1 of 5 • next >
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Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... Yes, but also it has few functions for a seamless integration with few outputs from other packages: According to that Bioconductor vignettes link shared by @WouterDeCoster: > the tximport pipeline offers the following benefits: (i) this approach corrects for potential changes in gene length acr ...
written 26 days ago by sangram_keshari120
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Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... Yes, this pipeline is a better choice. ...
written 27 days ago by sangram_keshari120
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Answer: A: Graphical output of Blast. What are grey and black lines?
... The vertical line is a separation of the single sequence with different alignment score and the horizontal line between green and red is a separation in the same sequence where alignment score is different for different regions. Hope that helped. ...
written 27 days ago by sangram_keshari120
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Answer: A: May I use numreads for doing DGE after quantifying by Salmon
... Basically, NumReads will have quantified reads mapped to each transcript. Yes, you can use them. Once quantified, You can use other tools like - `edgeR` and `DESeq2` for DEG. ...
written 27 days ago by sangram_keshari120
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Comment: C: General Question to shRNA-Seq analysis
... May I know, You want to compare conditions or have a control to compare with? In terms of Matrix design. Yes, if you doing with multiple conditions then the second command will come handy. ...
written 27 days ago by sangram_keshari120
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Comment: C: mutual rank values for distance matrix formation for co-expression analysis
... I suppose, If you do have RAW expression values then also you can create co-expression matrix! ...
written 6 weeks ago by sangram_keshari120
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Comment: C: Identifying novel isoforms from RNAseq data
... Yes, I completely agree. Even I encourage people to do with StrigTie (Because of its improvements in efficiency) As a matter of doubt in the question dealing with Cufflinks, I tried to explain where it might be going wrong. ...
written 6 weeks ago by sangram_keshari120
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Answer: A: Identifying novel isoforms from RNAseq data
... Have tied to look at all the options how to find novel transcripts using Cufflinks? In that case, I think you might be missing the following things - This is from [Cufflinks manual][1]. > `-g/–GTF-guide ` > > Tells Cufflinks to use the supplied reference annotation a GFF file to &g ...
written 6 weeks ago by sangram_keshari120
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Comment: C: How do transcript-level gene ontology
... Then to my knowledge, DAVID or for that case, any popular Gene Ontology tool is capable of taking Ensemble IDs into account. So you can directly use Ensemble IDs, No need of converting them to any gene ID. ...
written 6 weeks ago by sangram_keshari120
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Comment: C: How do transcript-level gene ontology
... May I know which species you dealing with? ...
written 6 weeks ago by sangram_keshari120

Latest awards to sangram_keshari

Scholar 6 months ago, created an answer that has been accepted. For A: cuffcompare: No novel genes found. Is this possible?
Supporter 10 months ago, voted at least 25 times.
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

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