User: serpalma.v

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serpalma.v10
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New User
Location:
Germany
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1 week ago
Joined:
3 years, 9 months ago
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Posts by serpalma.v

<prev • 24 results • page 1 of 3 • next >
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Comment: C: How to find the self aligned repeat region in human genome
... Is there any similar data set for Bos taurus (UMD3.1)?. I've browsed UCSC and Ensembl corresponding directories. ...
written 22 days ago by serpalma.v10
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Comment: C: Feasible Annotation of 4 million unique SNPs
... Thank you Emily, besides the long time to complete the job, is there another negative aspect to run such many variants with the online tool? ...
written 5 weeks ago by serpalma.v10
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Comment: C: Feasible Annotation of 4 million unique SNPs
... Thank you very much Maxime, the annotations were finished overnight with ensembl tool VEP. I will keep ANNOVAR in mind nevertheless for the future. ...
written 5 weeks ago by serpalma.v10
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Feasible Annotation of 4 million unique SNPs
... I ran the GATK tool ASEReadCounter to measure allele specific expression (ASE). There were 100 BAM input files processeced by ASEReadCounter. The output (ASE file) is a table for each input file with read counts for the reference allele and the alternative allele (SNP). However, there are no annota ...
gatk ase snp written 5 weeks ago by serpalma.v10 • updated 5 weeks ago by Emily_Ensembl12k
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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 months 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 months 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 months 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 13 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 13 months ago by serpalma.v10 • updated 13 months ago by genomax32k
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Comment: C: Assigning time to data analysis (detection of signatures of selection)
... Ilumina HiSeq 2000, 30x coverage ...
written 13 months ago by serpalma.v10

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