User: prince26121991

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Posts by prince26121991

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Comment: C: BLAST nr database
... You will have to download ftp://ftp.ncbi.nih.gov/blast/db/nr.00.tar.gz , ftp://ftp.ncbi.nih.gov/blast/db/nr.01.tar.gz, ftp://ftp.ncbi.nih.gov/blast/db/nr.02.tar.gz ......... ftp://ftp.ncbi.nih.gov/blast/db/nr.142.tar.gz all these file. Extract all of them and then run your command. Just provide t ...
written 3 months ago by prince2612199170
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Comment: C: BLAST nr database
... I am not sure but seems like memory error, please mention the size of available RAM in system. ...
written 3 months ago by prince2612199170
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Comment: C: NR annotation and Uniprot annotation
... I will not suggest you to consider uniprot result in this kind of case. Because if you think logically, I am offering 2 types of different flavor of ice-cream to child, then he has a option to select which one he likes, but if I am offering a single flavor to this child then he doesn't really have a ...
written 3 months ago by prince2612199170
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Answer: C: which ID of differentially expressed genes from the result page of the GEO2R is
... [Question: Which Ensembl protein id (ENSP) should I use? (Which id is used by string-db)][1] [1]: https://www.biostars.org/p/139709/#139719 ...
written 3 months ago by prince2612199170
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Answer: A: SnpEff database with maker annotation format
... Have you gave it a try? [The easiest way is to use the gffread program that comes with the Cufflinks software suite (Tuxedo)][1] [1]: https://www.biostars.org/p/45791/#90168 ...
written 3 months ago by prince2612199170
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Answer: A: Subsampling fastq.gz reads using reformat.sh changed all the quality scores?
... This is not weird, this is what it was supposed to do, reformat.sh itself says: Written by Brian Bushnell Last modified June 27, 2016 Description: **Reformats reads to change ASCII quality encoding**, interleaving, file format, or compression format. Optionally performs additional functions such a ...
written 3 months ago by prince2612199170
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Answer: A: NR annotation and Uniprot annotation
... This is what I have tried based on your input: I ran blast on Uniprot sequence of Transposon TX1 uncharacterized 149 kDa protein OS=Xenopus laevis OX=8355 PE=4 SV=1 against NR database on NCBI. This is the result I got ![enter image description here][1] Where You can see the very first hit is same ...
written 3 months ago by prince2612199170
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Answer: A: How to obtain gene symbols from the result list of GEO2R?
... Try this I think it will solve your issue ![Click on Select columns][1] ![SELECT column which you want to kept][2] [1]: https://i.ibb.co/fXJJgpK/Screenshot-from-2019-12-10-14-55-07.png [2]:https://i.ibb.co/Rp37D0p/Screenshot-from-2019-12-10-15-02-02.png ...
written 3 months ago by prince2612199170
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Answer: A: Is there a file information dictionary for files downloaded from ENCODE through
... If you have followed the proper protocol for batch download then there must be a file name Metadata.tsv in each batch. This metadata file contains following information: File accession File format Output type Experiment accession Assay Biosample term id Biosample term name Biosample type Biosample o ...
written 6 months ago by prince2612199170
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Comment: C: Samtools (v 1.5) index: failed to create index after sorting by name
... But following solution doesn't give the answer of your question. Because I am also getting same error when sorting by name as described in"How to specify the sort based on name in samtools sort? " . But your error is totally different then what is expected. I am still curious why you are getting tha ...
written 7 months ago by prince2612199170

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