User: Rob

gravatar for Rob
Rob60
Reputation:
60
Status:
Trusted
Location:
Last seen:
12 hours ago
Joined:
1 year ago
Email:
a*******@gmail.com

Posts by Rob

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
170
views
0
answers
Comment: C: PacBio genome assembly with canu shorter than expected
... I assume Canu correct the reads by itself, so no, I didn't correct them. But I will try your tool, it seems useful. ...
written 22 days ago by Rob60
3
votes
0
answers
170
views
0
answers
PacBio genome assembly with canu shorter than expected
... Hi, I have ~70x PacBio reads and I did an assembly with Canu. I expected a 216 Mb genome but I got a 146Mb assembly of 465 contigs with 1.3G of unassembled data. I tried to modify some parameters, for overlap length or coverage, but I can't get an assembly which reach the size I wanted (it just in ...
genome assembly pacbio canu written 22 days ago by Rob60
1
vote
2
answers
276
views
2
answers
Comment: C: NGS BWA Installing
... You should try google ASAP. Without joke, bwa and a lot of bioinformatics tools are not in the linux core library, that's why you can't install them with apt. For install a tool which is not in those library you have to download the package directly from the tool's website and follow instructions. ...
written 3 months ago by Rob60
0
votes
1
answer
227
views
1
answers
Comment: C: Vcf files fields: AD vs DP4
... Yes, it's probably that.. I think I got the things, thanks for your help! ...
written 3 months ago by Rob60
0
votes
1
answer
227
views
1
answers
Comment: C: Vcf files fields: AD vs DP4
... Hi, You are right, I thought there was one values missing in the AD fields, but it's not. Here the description of the AD and DP4 field: ##FORMAT= ##FORMAT= The DP4 appears good, 4 values as expected. But for the AD field, why there is 3 values? The first appears to be for reference, and t ...
written 3 months ago by Rob60
1
vote
1
answer
268
views
1
answers
Comment: C: python: translate DNA sequences to protien sequences
... Did you try to write something? ...
written 3 months ago by Rob60
4
votes
1
answer
227
views
1
answer
Vcf files fields: AD vs DP4
... In Vcf file, generate by samtools mpileup, there is an AD field (Allelic depth). This field is suppose to replace the previous DP4 field (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases). But when I use -t DP4, AD in mpileup, I have a different number of values in ...
vcf samtools snp written 3 months ago by Rob60
0
votes
0
answers
729
views
0
answers
Comment: C: samtools v1.3: AD, ADF and ADR fields
... This sound like a good question, anybody have an answer to that ? ...
written 3 months ago by Rob60
0
votes
1
answer
209
views
1
answers
Answer: A: Calculating how many SNPs different Sequence A is to Sequence B, C, D etc...
... I think the fastest way is to use a tool which don't need a reference genome for finding your Snps (like DiscoSnp ++ http://colibread.inria.fr/software/discosnp/) and then compares them to each other for each of your datasets. ...
written 5 months ago by Rob60
1
vote
1
answer
270
views
1
answers
Comment: C: command line python script run on a file in different directory
... This is clearly not a problem of different directories between your file and the script, but mostly because you don't understand how scripts (and probably unix system) works. I suggest you to first read some unix tutorial and come here again with real bioinformatics question. ...
written 5 months ago by Rob60

Latest awards to Rob

Popular Question 3 months ago, created a question with more than 1,000 views. For How to properly merge multiple runs into one bam file ?
Supporter 5 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1067 users visited in the last hour