User: bioinforesearchquestions

Reputation:
120
Status:
Trusted
Location:
United States
Last seen:
2 days, 17 hours ago
Joined:
2 years, 1 month ago
Email:
b***********************@gmail.com

Posts by bioinforesearchquestions

<prev • 183 results • page 1 of 19 • next >
0
votes
0
answers
101
views
0
answers
Looking for WIG base coverage file for hg19 to call CNVs in Exome data using EXCAVATOR
... Hello folks, I am currently using EXCAVATOR2 for calling CNVs in the whole exome sequenced data for a trio samples. I am unable to access the wig file for hg19 reference "http://grimmond.imb.uq.edu.au/uniqueome/downloads/hg19_uniqueome.coverage.base-space.25.1.Wig.gz" from the link provided. Did a ...
exome excavator wig cnv hg19 written 13 days ago by bioinforesearchquestions120
0
votes
1
answer
561
views
1
answers
Comment: C: uniqueome mappability file for EXCAVATOR-tool
... Hi Canh, Which directory did you find the uniqueome mappability files? Are you referring to EXCAVATOR_Package_v1.1.2/data/ucsc.hg19.bw? ...
written 13 days ago by bioinforesearchquestions120
0
votes
1
answer
410
views
1
answers
Comment: C: Looking for wig base coverage file for hg19
... Hi Titus, Have you got a chance to download the h19 wig file? or Do you know any links where I can download it? ...
written 14 days ago by bioinforesearchquestions120
0
votes
1
answer
115
views
1
answers
Comment: C: Can I merge the exome interval lists from two different kits for identifying CNV
... Thanks, Sean for your help, I really appreciate it. Just for testing purpose, I used the Nextera Exome Capture bed file for both the trio (originally Nextera) and 50 (originally Nimblegen) exome samples. I got ~2000 CNVs from 50 samples and 340 CNVs from the trio samples. I will read both the pap ...
written 14 days ago by bioinforesearchquestions120
1
vote
1
answer
115
views
1
answer
Can I merge the exome interval lists from two different kits for identifying CNVs using XHMM?
... Hello folks, I am trying to call CNVs from trio (Father, Mother, Son) samples. Father and son are affected and mother is unaffected. I used XHMM (eXome-Hidden Markov Model) for calling CNVs in my exome sequenced reads. **XHMM uses principal component analysis (PCA) normalization and a hidden Markov ...
exome bed intervals xhmm cnvs written 14 days ago by bioinforesearchquestions120 • updated 14 days ago by Sean Davis23k
0
votes
0
answers
144
views
0
answers
Which read counts file from miRDeep2 should be considered for differential expression analysis?
... Hello everyone, I would appreciate some help with my data. I want to do Differential Expression profiling for miRNA samples. Using the miRDeep2 program and algorithm, I'm in trouble when dealing with results to make a proper table in order to use it as input for DE software such as EdgeR or DEseq ...
mirbase mirdeep2 rna-seq mirna written 22 days ago by bioinforesearchquestions120
0
votes
1
answer
608
views
1
answers
Answer: A: Read Counts from miRDeep2 for posterior DE analysis
... Hi V82masae, I am having the same issue, 1) Should I use all_samples.csv or result.csv as read count? miRNAs_expressed_all_samples_14_09_2016_t_15_05_38.csv and result_14_09_2016_t_15_05_38.csv 2) Did you consider both miRNAs or just one? ...
written 22 days ago by bioinforesearchquestions120
0
votes
0
answers
176
views
0
answers
Do I need to provide the Illumina's target region bed file for qualimap?
... Hi friends, I have trio exome sequencing data with me. In order to know the coverage for trio samples. I used qualimap tool. Why is the mean coverage very low only 5.3X. Generally, exome sequencing have 80-100X coverage right. I didn't provide the reference file for the tool. Do I need to provide t ...
1
vote
0
answers
203
views
0
answers
Comment: C: Help required for Bacterial RNAseq data
... Thanks, Kevin. I will first run trinity and see what are all the output files I am going to get. ...
written 28 days ago by bioinforesearchquestions120
0
votes
2
answers
189
views
2
answers
Comment: C: How come the QC-passed reads from samtools flagstat is different from FASTQ (R1+
... Thanks. I am looking for alignment percentage, Isn't it this number misleading? If I want the alignment rate, do I report 30.12% or 24.35% (21.05% + 3.30%)? ...
written 5 weeks ago by bioinforesearchquestions120

Latest awards to bioinforesearchquestions

Popular Question 7 days ago, created a question with more than 1,000 views. For How to visualize large VCF files
Popular Question 23 days ago, created a question with more than 1,000 views. For How to visualize large VCF files
Popular Question 5 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Popular Question 6 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Popular Question 7 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Popular Question 12 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Supporter 12 months ago, voted at least 25 times.
Centurion 12 months ago, created 100 posts.
Popular Question 13 months ago, created a question with more than 1,000 views. For Applying hard filters for variants

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1408 users visited in the last hour