User: joneill4x

gravatar for joneill4x
joneill4x40
Reputation:
40
Status:
New User
Location:
Canada
Last seen:
1 day, 15 hours ago
Joined:
4 years, 1 month ago
Email:
j********@gmail.com

Posts by joneill4x

<prev • 22 results • page 1 of 3 • next >
2
votes
1
answer
124
views
1
answer
mutations causing predicted gene loss of function in healthy individual - WGS
... Just for interest, I had my whole genome re-seqeunced (BGISEQ-500, 30X coverage). Variants were called with GATK and the variants were annotated with SnpEff and annovar. SnpEff also predicted the functional effects of the variants. Interestingly, there are hundred of variants that are predicted c ...
genome sequencing annoation written 4 weeks ago by joneill4x40 • updated 4 weeks ago by Pierre Lindenbaum121k
1
vote
2
answers
1.2k
views
2
answers
Answer: A: Align paired and unpaired reads simultaneously using Bowtie2?
... Like this: bowtie2 -x btInd -1 13_trimmed_R1.fastq.gz -2 13_trimmed_R2.fastq.gz -U 13_unpaired_1.fastq.gz,13_unpaired_2.fastq.gz -p 12 | samtools sort -@ 12 -T temp -o 13trimmed_sorted.bam Works for me. (bowtie2 version 2.3.2) ...
written 4 months ago by joneill4x40 • updated 4 months ago by ATpoint19k
0
votes
1
answer
886
views
1
answers
Comment: C: Figuring out HiC restriction enzyme
... Can you go into further detail how you figured it out gbdias? I am in the same situation as you were. There are 20 over-represented 7-mers located near the start of my reads. (Both for forward reads and reverse reads). How do I used this data to deduce the restriction enzyme cutting site? ...
written 11 months ago by joneill4x40
1
vote
1
answer
803
views
1
answers
Comment: C: Extract PE Reads (with their mates) supporting variants in vcf file
... Haha! Unfortunately, there will be no article written, but seeds will sprout and thrive thanks to your help. ...
written 12 months ago by joneill4x40
1
vote
1
answer
803
views
1
answers
Comment: C: Extract PE Reads (with their mates) supporting variants in vcf file
... This was just what I needed as well! It was a huge help, at just the right time! Thank you Pierre! All I had to do was manually edit the VCF file 'src/test/resources/S1.vcf.gz' so that it would reflect my target variant. ...
written 12 months ago by joneill4x40
0
votes
1
answer
29k
views
1
answers
Comment: A: How To Get The Subclusters From The Object Of Hclust() Using Cutree() According
... Thank you, this was really helpful. EDIT: this was meant to be under seidel's answer. ...
written 17 months ago by joneill4x40
0
votes
0
answers
593
views
0
answers
unitigs for proovread
... "Unitigs are high-confidence assembly fragments produced by for example ALLPATHS, Meraculous2 or the Celera Assembler. In contrast to contigs, unitigs don’t extend past any conflict in the underlying short read data, making them highly reliable." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609002/ ...
proovread illumina idba_ud written 2.8 years ago by joneill4x40
0
votes
3
answers
2.7k
views
3
answers
Comment: C: Newbler 3 assembler download - assembly of highly heterozygous genome
... Hi lexnederbragt, thanks for your answer. I tried using that link again just now, but it still is showing only v2.9 available for download. ...
written 2.8 years ago by joneill4x40
1
vote
3
answers
2.7k
views
3
answers
Newbler 3 assembler download - assembly of highly heterozygous genome
... Hello all, Does anyone know where I can obtain a copy of the Newbler v3.0 assembler? I have managed to download and install v2.9, having obtained it from from the 454 official website. Link: http://454.com/contact-us/software-request.asp However, v2.9 has a max read length of 2000, while v3.0 ...
newbler assembly written 2.9 years ago by joneill4x40 • updated 16 months ago by salgado70
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Detecting gene duplication in de-novo assembly
... OK! I'll give that a try. Thanks Wouter! ...
written 3.1 years ago by joneill4x40

Latest awards to joneill4x

Popular Question 11 months ago, created a question with more than 1,000 views. For Detecting gene duplication in de-novo assembly
Popular Question 12 months ago, created a question with more than 1,000 views. For Detecting gene duplication in de-novo assembly
Popular Question 2.2 years ago, created a question with more than 1,000 views. For De novo genome assembly strategy
Popular Question 2.8 years ago, created a question with more than 1,000 views. For De novo genome assembly strategy

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 627 users visited in the last hour