User: sangram_keshari
sangram_keshari • 120
- Reputation:
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- sangram_ksahu
- Last seen:
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- 1 year, 10 months ago
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Bioinformatics Student, Working in the field of Computational Genomics.
Posts by sangram_keshari
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... 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_keshari • 120
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... Yes, this pipeline is a better choice. ...
written 27 days ago by
sangram_keshari • 120
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... 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_keshari • 120
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... 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_keshari • 120
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... 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_keshari • 120
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... I suppose, If you do have RAW expression values then also you can create co-expression matrix! ...
written 6 weeks ago by
sangram_keshari • 120
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... 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_keshari • 120
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... 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_keshari • 120
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... 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_keshari • 120
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... May I know which species you dealing with? ...
written 6 weeks ago by
sangram_keshari • 120
Latest awards to sangram_keshari
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6 months ago,
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For A: cuffcompare: No novel genes found. Is this possible?
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10 months ago,
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