User: Curiosity

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Curiosity120
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http://interpretdata.b...
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8 years, 10 months ago
Joined:
8 years, 12 months ago
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Programmer, Bio-entrepreneur

Posts by Curiosity

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Homer ...Software For Motif Discovery And Next Generation Sequencing Analysis
... Homer also producing different results all the time and have lot f bugs in quality control step for RNA-Seq data. Watch out for these. ...
written 8.9 years ago by Curiosity120
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Comment: C: How To Deal With Un-Used Reads After De Novo Assembly?
... How did u get different bubbles in ggplot ? Do you mind sharing the command. Thanx! ...
written 8.9 years ago by Curiosity120
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What Mapping Quality Read Should I Use For Down Stream Rna-Seq Analysis
... I have 119 million mapped reads (38 million unique (who has same start and end) reads). 66 million of them have mapping quality >0 (23 million unique reads). Which file I should select for my downstream RNA-Seq analysis of the below and why? 1. All reads (119 m) 2. All unique reads (38 m) 3. A ...
rna written 8.9 years ago by Curiosity120 • updated 8.9 years ago by Anna80
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Comment: C: Bioscope Vs Bowtie+Tophat
... @GWW- How do you know whther reada are clipped are not (by looking at the length)?, I didn't quiet unsderstand the purpose of the question. @Leszek - If I filter non-redundant/duplicate (the reads that have same chr-start and chr-end) reads, 180 mil becomes 38 million in Bioscope case. In Tophat, 38 ...
written 8.9 years ago by Curiosity120
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Bioscope Vs Bowtie+Tophat
... Bioscope is giving 180 million mapped reads and bowtie+tophat is 38 million. The data is strand specific SOLID data (~50 bp). Does any one about this mapping differences ? ...
rna written 8.9 years ago by Curiosity120 • updated 8.9 years ago by Darked894.2k
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Comment: C: What Is A Whole Genome Background In Analysis Of Motifs Or Peaks?
... I quiet don't understand your answer. Could you please elaborate more. Or you mean this, there are sequences that are missed by sequencing machines so that we can use them as a good background ? ...
written 8.9 years ago by Curiosity120
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Answer: A: How To Convert Refseq Id To Gene Symbol For Non-Coding Rnas
... You can download all these annotations from Ensembl http://asia.ensembl.org/biomart/martview/67bf1defc1d2b3e205f0fd5f4506f849 And then use the following command grep NR_* filename ...
written 8.9 years ago by Curiosity120 • updated 8.9 years ago by Pierre Lindenbaum130k
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Answer: A: How To Convert Refseq Id To Gene Symbol As Pitx1
... You could download refseq gene list in "all" format instead of "BED" format using Galaxy http://main.g2.bx.psu.edu/ and then print the selected columns using unix command. Use the following command awk '{print $2"\t"$13}' all_refseq.list Ex: NM_001195025 Nuak2 ...
written 8.9 years ago by Curiosity120
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Comment: C: How To Plot Splicing Map
... Totally agree. . ...
written 8.9 years ago by Curiosity120
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Comment: C: How To Plot Splicing Map
... I think it is not like "average gene analysis". Because the intron length is constant but not the exon. Yes there is a brief description available regarding this plotting, i.e. "normalized complexity" which will highlight common features shared by multiple transcripts. ...
written 8.9 years ago by Curiosity120

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