User: Biogeek

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Biogeek400
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Posts by Biogeek

<prev • 186 results • page 3 of 19 • next >
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Get -400bp to +50bp sequence of gene from gff3 file
... Dear all, I have used bedops and bedtools to obtain -2000bp upstream of my gene start (based on gff3 coordinates) file and the scaffold fasta file of the genome.While I know how to get upstream, I do; however want to get per say +50bp upstream of the gene start too. Is there a way of getting the re ...
upstream promoter downstream motifs written 17 months ago by Biogeek400 • updated 17 months ago by Alex Reynolds30k
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Gene correlation analysis after deseq2
... I have 8 RNA libraries (4 reps per each of two conditions - tissue specific). I have approx 500 genes upregulated and 100 genes downregulated in the tissue of interest. I have a matrix of deseq2 normalised counts for all of the genes which I've pulled the differently expressed gene records from. ...
deseq2 correlation clustering written 18 months ago by Biogeek400 • updated 18 months ago by dqz3779779050
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Multiple fasta file : calculate % composition of amino acids
... I've come across Expasy protein param... it's limited in the sense you can only copy/paste 1 sequence at a time. Is there an alternative approach via command line to calculate alphabet % composition of each >sequence? I haven never ventured into Biopython. I mostly use R and command line. All he ...
calculate amino acids composition written 19 months ago by Biogeek400 • updated 19 months ago by Pierre Lindenbaum129k
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Comment: C: Refseq accessions - getting gene function and GO terms for each one
... GFF3 version 1.21 NW_018384101.1 RefSeq region 1 1835033 . + . ID=id0;Dbxref=taxon:1720309;Name=Unknown;chromosome=Unknown;collection-date=Mar-2014;country=Saudi Arabia: KAUST;gbkey=Src;genome=genomic;isolate=CC7;isolation-source=whole animal;mol_type=genomic DNA NW_018384101.1 Gnomon gene 12260 3 ...
written 19 months ago by Biogeek400
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Refseq accessions - getting gene function and GO terms for each one
... Can someone please let me know how I can get access to refseq gene names/functions and GO (CC,BP,MF) information for each gene using information gained from refseq accessions / information within the gff3. Many thanks. ...
gene function gene ontology refseq written 19 months ago by Biogeek400
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Refseq vs original genome assembly and issues
... A long winded post with multiple questions to gauge the consensus of the 'correct' approach to RNA-seq alignment when there is a Refseq vs published assembly version of a genome present. I've got the scenario where there is a published genome available as V1.0 and V1.1 (Genbank), and also on refseq ...
annotation genome alignment refseq written 19 months ago by Biogeek400
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Comment: C: STAR two -pass mode - lower alignment rate than one pass mode?
... If anyone wants to know why... see below: > Some drop in the uniquely mapped reads in the 2nd pass is to be > expected, but it's typically ~1-2%. It's caused by the reads with > short splice ovehangs, which can be mapped to multiple junctions. ...
written 19 months ago by Biogeek400
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STAR two -pass mode - lower alignment rate than one pass mode?
... Hi guys, Quick question. I've performed a two-step alignment with STAR 2.6a. It seems my unique alignment rates are approx 1% (85%) lower when performing two pass, than the original one pass mode (86%). I thought the aim of two-pass mode was to increase the number of reads mapping to novel splice j ...
two pass mode alignment star written 19 months ago by Biogeek400
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Comment: A: extract information from Uniprot
... Google: retrieve uniprot mapping. Any luck? Tell us what you have as your identifiers/ file formats. Print the head of your list/file. ...
written 19 months ago by Biogeek400
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Answer: A: Best tools to search for and report all alignments
... Subread align or STAR with custom settings to your desire? . These two are pretty fast and accurate.subread slightly pipping STAR according to literature ...
written 19 months ago by Biogeek400

Latest awards to Biogeek

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Any tools out there for Interproscan enrichment analysis?
Popular Question 7 months ago, created a question with more than 1,000 views. For Any tools out there for Interproscan enrichment analysis?
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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Parsing uniprot .dat files

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