User: erdiazval

gravatar for erdiazval
erdiazval10
Reputation:
10
Status:
New User
Location:
Last seen:
4 days ago
Joined:
4 months, 1 week ago
Email:
e********@gmail.com

Posts by erdiazval

<prev • 4 results • page 1 of 1 • next >
0
votes
3
answers
5.2k
views
3
answers
Answer: A: Tools For Analysis Allele Specific Expression In Rna-Seq Data?
... Hi Sara ASE is a complex task, the pipeline I developed and have being following is this (considering you have both the parental transcriptomes as well as the F1 hybrid transcriptomes: 1) Align parental transcriptomes against the Reference genome (STAR) 2) Call homozygous SNPs with depth > 4 rea ...
written 4 weeks ago by erdiazval10 • updated 4 weeks ago by GenoMax42k
0
votes
3
answers
561
views
3
answers
Answer: A: Extract several fields from vcf file
... I would go for using SNPSift program This is an instance of how I use it to extract: position, ref allele, alt allele, Allele Depth (AD from genotype field), and functional annotation by gene ID. !/bin/bash for i in *.vcf; do java -jar /data/software/snpEff/snpEff/SnpSift.jar\ extra ...
written 4 weeks ago by erdiazval10
1
vote
3
answers
288
views
3
answers
Answer: A: How to get counts data for allele specific expression analysis (ASE) from aligne
... The first step is to idetifying polymorphisms of your libraries against the reference genome. I would go for a pseudo-reference aproach which implies that you impute the homozygous SNPs of your libraries into the reference genome. Then you align your libraries against both the reference and the pseu ...
written 4 weeks ago by erdiazval10
0
votes
4
answers
1.4k
views
4
answers
Answer: A: Sleuth: Combined lrt and wt tests, clustered heatmap
... You can use the LTR to test for differential expression and get the log2 foldchange estimates from the kallisto normalized values while you don't include the filtered out values. SNM <- kallisto_table(so, use_filtered = TRUE, normalized = TRUE, include_covariates = TRUE ...
written 3 months ago by erdiazval10

Latest awards to erdiazval

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 730 users visited in the last hour