User: Buffo

gravatar for Buffo
Buffo470
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470
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15 hours ago
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1 year, 4 months ago
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Posts by Buffo

<prev • 142 results • page 1 of 15 • next >
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Comment: C: RNA-seq gene expression normalization for independent samples
... What about Transcripts per million? (TPM), or RPKM? (Reads per kilobase per million)? ...
written 1 day ago by Buffo470
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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 Buffo470
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Answer: A: Creating blast database blast+
... 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 Buffo470
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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 Buffo470
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Answer: A: Parse results of predicted miRNAs
... 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 Buffo470
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Answer: A: miRNA identification from RNA seq data
... Shorts reads from RNA-seq are not miRNAs, you have to prepare special miRNA library. ...
written 17 days ago by Buffo470
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Comment: C: restructure rows and columns in perl or python (Interleaving columns by row pair
... 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 Buffo470
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Comment: C: restructure rows and columns in perl or python (Interleaving columns by row pair
... > 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 Buffo470
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Comment: C: restructure rows and columns in perl or python
... 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 Buffo470
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UTR-DB accession numbers?
... 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 ...
utrdb dowloaddb accession written 11 weeks ago by Buffo470

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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