User: anu014

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anu014120
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India
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2 years, 3 months ago
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Posts by anu014

<prev • 95 results • page 1 of 10 • next >
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Comment: C: 5 prime & 3 prime end of the gene in GTF
... Thanks Emily for answering. ...
written 18 hours ago by anu014120
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Comment: C: 5 prime & 3 prime end of the gene in GTF
... So start of gene is always 5' end weather the gene is on reverse or forward ?? ...
written 7 days ago by anu014120
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5 prime & 3 prime end of the gene in GTF
... Hello Biostars! This one is just a basic question which is confusing me a lot. I've a GENCODE GTF & I'm pasting a record from it here: chr15 HAVANA gene 34341713 34343177 . - . gene_id "ENSG00000182117.5"; gene_type "protein_coding"; gene_name "NOP10"; level 1; havana_gene "OTTHUMG00000129 ...
genome gene sequence gencode ensembl written 7 days ago by anu014120
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Comment: C: Survey/Vote: If you could double the speed of any three commandline tools, which
... Sure @dhbradshaw. I should have done that. As we have got alternative for TrimGalore (Skewer). I would like to omit it now. **Trinity** is for de novo reconstruction of transcriptomes from RNA-seq data. We can mention Threads & memory in it. But still, it takes too much time even on a machine w ...
written 11 days ago by anu014120
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Answer: A: Skewer: a fast and accurate adapter trimmer for next-generation sequencing paire
... Doesn't this tool supports single-end data too? It claims "Targeted at Single End, Paired End (PE), and Long Mate Pair (LMP) reads" here : https://sourceforge.net/projects/skewer/ ...
written 11 days ago by anu014120
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Comment: C: Survey/Vote: If you could double the speed of any three commandline tools, which
... But doesn't it support only paired-end data? "Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-182) ...
written 11 days ago by anu014120
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Comment: C: Survey/Vote: If you could double the speed of any three commandline tools, which
... Wow! It supports multi-threading. I wasn't aware of this tool.Thanks @ATPoint! ...
written 11 days ago by anu014120
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Answer: A: Survey/Vote: If you could double the speed of any three commandline tools, which
... I would like to name these: 1. TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore ) - No parallel processing 2. Trinity (https://github.com/trinityrnaseq/trinityrnaseq/wiki ) 3. MAKER (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Tra ...
written 12 days ago by anu014120
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Comment: C: Difference between ncRNA & non_coding in GENCODE
... Is this the difference: 'non-coding' is transcribed till primary transcript & dies off whereas ncRNA is a mature RNA? ...
written 14 days ago by anu014120
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Comment: C: Difference between ncRNA & non_coding in GENCODE
... Hi Emily, Thanks for the reply. :) I was confirming about definition of 'non-coding' : "Transcript which is known from the literature to not be protein coding" . According to this definition, gene is getting transcribed but doesn't form protein. Isn't this same case as ncRNA (A non-coding RNA (ncRN ...
written 14 days ago by anu014120

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