User: rbronste

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rbronste160
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Posts by rbronste

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Comment: C: Filter HT-Seq output for gene subclasses
... Yes I had thought to do this however I don't believe biotype extends to such a subclass, mostly applies to protein_coding vs lncRNA vs miRNA genes etc etc ...
written 27 days ago by rbronste160
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Filter HT-Seq output for gene subclasses
... I was wondering about a straightforward way to filter RNA-seq datasets specifically those coming out of HT-Seq for highly expressed genes in specific subclasses, for instance all TFs (or all sequence specific binding factors) of absolute counts lets say higher than 100? Thanks! ...
htseq transcription factor rna-seq written 27 days ago by rbronste160
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Official gene symbol list to BED file
... Simply trying to generate an annotated bed file for a specific assembly only from a list of official gene symbols, in my case derived from DESeq2 results. Is there a pretty straightforward way to go about doing this? ...
bed gene symbol deseq2 written 4 weeks ago by rbronste160 • updated 4 weeks ago by Alex Reynolds22k
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Extracting interval from fasta header
... Hi, Im wondering about the most straightforward way to extract the interval information contained in a fasta header such as the one below, thanks! Also maybe to pipe into a newly created bed file. >Mouse|chr12:112380949-112381824 | element 3 | positive | neural tube[4/4] | hindbrain (rhomb ...
fasta bed header interval written 4 weeks ago by rbronste160 • updated 4 weeks ago by Alex Reynolds22k
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Comment: C: FIMO output to bed
... My apologies neglected to search back, however your response adds to my understanding of how to do this so thanks. ...
written 4 weeks ago by rbronste160
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FIMO output to bed
... Trying to figure out a good way to covert fimo output files such as the gff file to a standard bed4-6 file for use elsewhere. Was doing the following but it seems to generate an unusually structured bed file: sortBed -i fimo.gff | gff2bed > fimo.bed ...
bedtools fimo meme bedops written 4 weeks ago by rbronste160 • updated 4 weeks ago by kennethcondon20071.1k
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FIMO target coordinates in fasta file
... Wondering about a relatively quick and easy way to find the following FIMO given coordinates in a fasta file? Maybe output as a an actual chromosomal coordinate? Thanks! pattern name sequence name start stop strand score p-value q-value matched sequence MA0432.1 mm10_d ...
fasta fimo meme motif written 5 weeks ago by rbronste160
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Comment: C: Table browser +/- 2Kb of TSS export
... Its strange but when I do this backwards and forwards with my refGene.tss.padded.bed and target "intervals.bed" I get that answer.bed is a full overlap, for instance if my intervals.bed has 1000 intervals and refGene.tss.padded.bed has 39702 intervals and I do the following: bedops -n 1 refGene ...
written 6 weeks ago by rbronste160
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Comment: C: Table browser +/- 2Kb of TSS export
... Thanks again! One final question, in this particular instance if I want to use the refGene.tss.padded.bed file as a drop out, for instance take a set of intervals and drop out refGene.tss.padded.bed intervals what would be the most straightforward way to do that? Just want a final bed file without t ...
written 6 weeks ago by rbronste160
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Comment: C: Splitting .bed file by genomic location
... Any other ideas? Thanks! ...
written 6 weeks ago by rbronste160

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Centurion 6 months ago, created 100 posts.
Rising Star 9 months ago, created 50 posts within first three months of joining.
Supporter 9 months ago, voted at least 25 times.

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