User: Nano

gravatar for Nano
Nano20
Reputation:
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New User
Location:
Finland
Last seen:
4 years, 2 months ago
Joined:
4 years, 7 months ago
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Posts by Nano

<prev • 9 results • page 1 of 1 • next >
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(Closed) New in Bioinformatics, Where to start with RNA-Seq
... I just graduated as a Bioinformatician, I realized that we have learnt so little that I can not compete in the Job field. I realized that most of the requirements by companies and research institutes who hire Bioinfotmaticians are mostly NGS, RNA-Seq data analysis and related things. Pretty much all ...
ngs rna-seq written 4.3 years ago by Nano20
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Outputing a Blast result that includes global pairwise alignment
... I have made a Local Blast of one query file (containing thousands of sequences) against many individual database formatted files (each containing thousands of sequences). the result is good. script below #!/bin/bash for file in *.fasta do   pb tblastn -query queryFile.fasta -dbnuc $file -out $file ...
alignment blast bash written 4.4 years ago by Nano20
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Answer: A: Local Blast Database
... The problem with concatenation is that it will produce a single file, I am required to find the expression level of each query sequence from each of file among the 150 files. if i concatenate them, the result wont specify the expression on each file, so i need to create a database for every file and ...
written 4.5 years ago by Nano20
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Local Blast Database
... I need to blast one protein query file against 150 nucleotide files. at first I tried Blast but it says there is not database, I created a database with one of the 150 files and blasted against it, it worked! So How do I loop through the 150 files and create a database of each of them so that the q ...
sequence alignment blast written 4.5 years ago by Nano20
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(Closed) Find and replace
... I am working with a group of gene names which I want to convert to their GenBank accession numbers. I have them sorthed out already: the first column is in GenBank, the second column is the gene names which i want to replace. FJ176297 B6DXA9 FJ176298 B6DXB0 BABH0103 ...
gene alignment written 4.6 years ago by Nano20
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I need help to fix this script, it runs nicely but gives error message that i am not able to fix.
... `~/Documents/Blast/makeblastdb -in Bmori.fst -dbtype nucl -out Bmori_BlastDB -parse_seqids`; ## Creating Bmori database $BLAST_DB='Bmori_BlastDB'; ## storing in a variable @QUERY_FILES=`ls *.fas`; ## list all the transcriptomes of different species foreach $tmp (@QUERY_FILES) {         #print "$t ...
gene blast written 4.6 years ago by Nano20 • updated 4.6 years ago by Jean-Karim Heriche22k
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Comment: C: blasting a nucleotide query file (about 2000 seq) over a group of transcriptomes
... Thanks so much guys ...
written 4.6 years ago by Nano20 • updated 6 months ago by RamRS27k
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Comment: C: blasting a nucleotide query file (about 2000 seq) over a group of transcriptomes
... Do you have any idea or hints on how i can go about that..? I will really appreciate ...
written 4.6 years ago by Nano20
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blasting a nucleotide query file (about 2000 seq) over a group of transcriptomes files
... I have a query file containing around 2600 nucleotide sequences. and another group of transctiptomes files (over 150 files) containing hundreds of thousands of sequences in each file. I need to blast the query file over the transcriptomes files to determine which gene in the query file is found (exp ...
gene tutorial alignment blast written 4.6 years ago by Nano20 • updated 2.9 years ago by Biostar ♦♦ 20

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