User: serpalma.v

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serpalma.v10
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10
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New User
Location:
Germany
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2 weeks, 5 days ago
Joined:
3 years, 5 months ago
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Posts by serpalma.v

<prev • 20 results • page 1 of 2 • next >
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Chromosome Names in genome are incompatible with annotations
... Dear community, while creating an index for the bovine genome with STAR, the process fails because the chromosome names in the annotation file (Bos_taurus.UMD3.1.87.gtf) are incompatible with the ones in the reference file (UMD3.1_chromosomes.fa) (e.g. for chromosome "10" vs "gnl|UMD3.1|GK000010.2 ...
alignment star written 5 weeks ago by serpalma.v10
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Comment: C: basic concepts behind --sjdbOverhang (STAR)
... Thanks John, I uderstand your point. I could try that, but I need to understand what I am doing, so that later I can fully trust my results. ...
written 5 weeks ago by serpalma.v10
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basic concepts behind --sjdbOverhang (STAR)
... Dear community, after reading the manual and several threads (google: --sjdbOverhang), I still do not feel confortable using this option. I understand the instructions for --sjdbOverhang as that it sets the max number of bp on each side of an exon-exon junction. And that is determined by the max le ...
star sjdboverhang written 5 weeks ago by serpalma.v10
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Comment: C: How to project the read count?(HiSeq2500, mouse genome, resequencing)
... There I get (for 30x coverage): Output Required: 85,714,285,714 bases But the number of reads required is not shown. Should I jus devide Output Required by the length of reads? ...
written 9 months ago by serpalma.v10
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How to project the read count?(HiSeq2500, mouse genome, resequencing)
... Dear community, we have been ask to project the read count for our samples, we have to select between: - 1 flow cell - 1 lane - more than one flow cell - between 1 flow cell and 1 lane We have 6 mouse lines, 10 individuals in each one. So we have 60 samples. I am new to this, but I read up a ...
genome sequence next-gen snp sequencing written 9 months ago by serpalma.v10 • updated 9 months ago by genomax226k
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Comment: C: Assigning time to data analysis (detection of signatures of selection)
... Ilumina HiSeq 2000, 30x coverage ...
written 9 months ago by serpalma.v10
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Assigning time to data analysis (detection of signatures of selection)
... Dear community We are currently writing a grant proposal where we intend to sequence the genome of 6 mouse lines with 10 individuals per line, then process the data to the point where we can detect signatures of selection by calculating iHS and FST statistics. (based on: http://www.ncbi.nlm.nih.gov/ ...
next-gen snp sequencing written 9 months ago by serpalma.v10
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What is the language of this mass spectrophotometry data processing output file
... Dear community, I have been assigned a task to retrieve information from files that were processed from raw mass spectrophotometry data (file.mzML). These files have just ".data" as extension and when I open them, I cannot recognize the language and therefore I cannot load them into R and work on t ...
mass spectrophotometry output written 12 months ago by serpalma.v10 • updated 12 months ago by Pierre Lindenbaum92k
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Discrepancy in gene set size between gage() and geneData()
... Dear community,  I have run GAGE and Pathview  on my microarray data. Everything worked fine. However, the number of genes assigned to a kegg pathway after using the gage() function is different from the number of genes produced by the geneData() function, which is the function to use in order to ...
pathview gage kegg pathway analysis written 14 months ago by serpalma.v10
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Comment: C: What test to apply to detect genomic signatures of selection?
... Thanks. We will collect DNA from the last generation only.  ...
written 15 months ago by serpalma.v10

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Popular Question 12 months ago, created a question with more than 1,000 views. For topGO approach for a list a genes without expression
Popular Question 2.4 years ago, created a question with more than 1,000 views. For topGO approach for a list a genes without expression
Popular Question 2.4 years ago, created a question with more than 1,000 views. For P1 And A Adater Trimming And Mapping From Ion Torrent Reads

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