User: Buffo
Buffo • 470
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Posts by Buffo
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... What about Transcripts per million? (TPM), or RPKM? (Reads per kilobase per million)? ...
written 1 day ago by
Buffo • 470
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Comment:
C: miRNA analysis by miRDeep2
... As first approach I would recommend you doing by yourself, you can download mirna database from [mirdb][1], and then map your reads (each sample) to the database with [bowtie][2], after that you can count reads mapped to the mirDB with [samtools][3] idxstats or [htseq][4], normalize and found differ ...
written 10 days ago by
Buffo • 470
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... You may try using concatenate "cat":
cat file1.fasta file2.fasta file3.fasta > my_all_files.fasta
Then you can make your complete DB. ...
written 14 days ago by
Buffo • 470
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Comment:
C: VCF miner Installation
... when I think my life has no sense I like to loggin here and read your comments Wouter, you're absolutely pathetic spending time writting about nothing and helping to nobody, and your auto-up-votes is the best :).
In your curriculum write about your score in biostars (20 k) it would be very helpfull ...
written 14 days ago by
Buffo • 470
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... Something like this? [micro_rna.org][1] or this? [mirtarbase][2] or this? [mirdb][3].. or mirwalk, etc, etc, You can just download .xls files and sort as you wish..
[1]: http://www.microrna.org/microrna/getDownloads.do
[2]: http://mirtarbase.mbc.nctu.edu.tw/php/download.php
[3]: http://mir ...
written 17 days ago by
Buffo • 470
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... Shorts reads from RNA-seq are not miRNAs, you have to prepare special miRNA library. ...
written 17 days ago by
Buffo • 470
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238
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... You are a very funny person WouterDeCoster :). I'm glad you're learning to program but, in addition to online courses I recommend using common sense, sometimes it is very useful!
Best. ...
written 11 weeks ago by
Buffo • 470
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... > Also, it allows specifying both the output name and output directory.
prefix = sys.argv[1].split('.')[0]
output = open(prefix + '_output.txt', 'w') #you will never have to specify output name or directory
> you should use the 'with' statement for opening files
??? Why? ...
written 11 weeks ago by
Buffo • 470
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1
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... More profesional use .write:
import sys
output = open('output.txt', 'w')
with open(sys.argv[1]) as input:
while True:
line1 = [item for item in input.readline().split()]
if len(line1) == 0:
break
line2 = [item for item in input.readline().split( ...
written 11 weeks ago by
Buffo • 470
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... Hi everybody,
Somebody has worked with UTR-DB? I`m working with miRNA target prediction, so I need 3' UTRs, this is available on UTRdb, but each sequence name corresponds to accession number and locus which is absolute useless, I need the name of the protein that corresponds to that UTR for each se ...
written 11 weeks ago by
Buffo • 470
Latest awards to Buffo
Supporter
11 days ago,
voted at least 25 times.
Scholar
3 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Centurion
3 months ago,
created 100 posts.
Scholar
7 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
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