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Search: Posts Made By: floydian_slip
Forum: Bioinformatics 11-10-2020, 06:04 AM
Replies: 0
Views: 614
Posted By floydian_slip
get rsID or positions from variant name/gene info

Hi,
I have a list of variant and gene info as follows:

MCOLN1 c.406-2A>G
G6PC c.247C>T
PCDH15 c.733C>T
CLRN1 c.144T>G
NEB c.7431+1917_7536+372del

I would like to...
Forum: Bioinformatics 10-18-2020, 01:34 PM
Replies: 0
Views: 714
Posted By floydian_slip
get cDNA start and end for exons in a list of genes

Hi,
I have a list of genes for which I would like to list the cDNA start and end (c. notation) for each of the exons in them. I already have the genomic coordinates of exons in those genes using...
Forum: Bioinformatics 08-13-2020, 07:42 AM
Replies: 0
Views: 769
Posted By floydian_slip
Get Allele freq quickly from Gnomad

Hi,
I would like to know the AF of ~4000 rsIDs (dbSNP) quickly in Gnomad GRCh37 database. I looked at the instructions for getting this from Gnomad and it seems I would need to download the entire...
Forum: Bioinformatics 02-11-2020, 01:12 PM
Replies: 0
Views: 632
Posted By floydian_slip
Confusing Picard HsMetrics ON_BAIT_VS_SELECTED for near=250 and near=0

Hi, for an assay developed by my vendor, I ran latest Picard HsMetrics (2.21.8) with two different options for the same set of BAM files: one with a NEAR_DISTANCE=250 and one with NEAR_DISTANCE=0....
Forum: Bioinformatics 07-10-2012, 01:44 PM
Replies: 0
Views: 3,445
Posted By floydian_slip
Normalization of small RNA data for library size

Hi,
I have a few libraries of small RNA reads with different read counts: some libraries have more than 10 million reads, some others have <1 million. I wanted to normalize them for their sizes only...
Forum: Bioinformatics 07-02-2012, 08:47 AM
Replies: 2
Views: 2,305
Posted By floydian_slip
Thanks dariober, that works! thanks a lot! Best

Thanks dariober, that works! thanks a lot!
Best
Forum: Bioinformatics 06-29-2012, 11:16 AM
Replies: 2
Views: 2,305
Posted By floydian_slip
Not report promiscuous reads in bowtie

Hi,
I was wondering if there is a way in bowtie to stop further alignment of short reads that have already mapped to more than a certain number of locations. Say I have a read that has aligned...
Forum: Bioinformatics 06-29-2012, 11:10 AM
Replies: 0
Views: 1,150
Posted By floydian_slip
delete reads that dont overlap with any other reads

Hi,
I am a beginner to this area. I have an alignment file in bam/sam format after aligning short reads to my genome of interest using bowtie. I was wondering if there are any tools (or a way by...
Forum: RNA Sequencing 06-27-2012, 10:58 AM
Replies: 0
Views: 1,037
Posted By floydian_slip
delete reads that dont overlap with any other reads

Hi,
I am a beginner to this area. I have an alignment file in bam/sam format after aligning short reads to my genome of interest using bowtie. I was wondering if there are any tools (or a way by...
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