User: Biogeek

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Biogeek330
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Posts by Biogeek

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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 1 day ago by Biogeek330
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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 1 day ago by Biogeek330
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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 1 day ago by Biogeek330
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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 2 days ago by Biogeek330
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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 3 days ago by Biogeek330
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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 6 days ago by Biogeek330
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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 6 days ago by Biogeek330
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Comment: C: small FASTa file from genome guided trinity assembly?
... Any code/ commands you can paste from your Trinity run? Trinity uses fastq and outputs fasta. You then use your fastq reads and count the read alignments with RSEM. So I'm not sure why you are running RSEM data in Trinity...?? Do you mean you used a particular Trinity pipeline rather than the asse ...
written 6 days ago by Biogeek330
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Comment: C: NCBI genome version vs published genome version - what's 'better'?
... genomax. I agree BUT... what if this species has many clade-specific genes. Surely refseq will become a limiting database/ step?? ...
written 7 days ago by Biogeek330
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Comment: C: NCBI genome version vs published genome version - what's 'better'?
... Thanks for your time jrj.healey. I imagined that the NCBI version had been more conservatively reviewed and curated - potential for discarding useful info. Now there is a Genbank and Refseq version. I think I will use V1.1 Genbank (GCA_*) as that's the official files which the authors of the genome ...
written 7 days ago by Biogeek330

Latest awards to Biogeek

Popular Question 21 days ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Popular Question 9 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
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Popular Question 9 months ago, created a question with more than 1,000 views. For Stand alone Blast annotation with multiple databases
Popular Question 9 months ago, created a question with more than 1,000 views. For Parsing uniprot .dat files
Popular Question 9 months ago, created a question with more than 1,000 views. For Going from BlastX to GO annotation
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Scholar 2.7 years ago, created an answer that has been accepted. For A: Visualize groups of conditions bys MDS.

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