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1,000 results • Page 4 of 20

Recent Votes

Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)

A: Mouse promoter regions

Answer: How to get information about promoter from bulk-RNAseq?

A: Extracting Flanking Regions across TSS using R scripts

A: Mouse promoter regions

A: Finding zebrafish promoters ENSEMBL

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Recent Replies

Comment: pal2nal -nogap -nomismatch options not working by Marie • 0

Hi, did you end up solving this? I am running into the same issue. Marie

Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130

and what about enhancer? is it possible to do it from a bulk-RNAseq?

Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130

yes! clearly the terminology on my side needs to improved!

Comment: How to get information about promoter from bulk-RNAseq? by rpolicastro 12k

Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …

Answer: How to get information about promoter from bulk-RNAseq? by Trivas ★ 1.2k

I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…

Comment: How to add annotation columns with specific colors to the heatmap? by Ram 39k

Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.

Comment: VCF file CSQ flag by Ram 39k

True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.

Comment: Creating a local version of Clustered NR database by PeterC_NCBI ▴ 260

@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…

Comment: Shannon's Entropy by Sliding Window in R by rohitsatyam102 ▴ 690

Hi Were u able to achieve this?

Comment: Differences in GTF files hg19 and hg38 by GenoMax 130k

Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…

Comment: VCF file CSQ flag by Pierre Lindenbaum 154k

if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…

Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b by Ram 39k

https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.

Comment: VCF file CSQ flag by Ram 39k

A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…

Comment: Differences in GTF files hg19 and hg38 by heureuse • 0

Thank you very much. I get it from UCSC.

Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b by Arup Ghosh 3.2k

This post does not fit the theme of this forum.

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