User: pablo

gravatar for pablo
pablo140
Reputation:
140
Status:
Trusted
Location:
Last seen:
2 days, 20 hours ago
Joined:
2 years, 2 months ago
Email:
v*************@hotmail.fr

Posts by pablo

<prev • 138 results • page 1 of 14 • next >
1
vote
0
answers
149
views
0
answers
Interpreting results of a dotplot
... Hello, I have an assembly with a size 1.9Gb . I expected a genome with a size around 1.1Gb. I supposed the excess is caused by heterozygosity (probably duplications) . To get an idea of that, I used `dgenies` to plot my assembly against itself. ![DotPlot][1] I got this dotplot. I got a good l ...
dotplot dgenies written 7 weeks ago by pablo140
0
votes
0
answers
289
views
0
answers
Comment: C: Using HiCanu assembler on PacBio Hifi reads
... I tried both assemblers on several data and all the time, I get better assemblies with hifiasm. ...
written 7 weeks ago by pablo140
0
votes
0
answers
289
views
0
answers
Comment: C: Using HiCanu assembler on PacBio Hifi reads
... I already tried hifiasm first, that's why I would like to try HiCanu now. In order to have a comparison of the two assemblies. ...
written 8 weeks ago by pablo140
0
votes
0
answers
289
views
0
answers
Using HiCanu assembler on PacBio Hifi reads
... Hello, I'm going to use HiCanu on PacBio reads. I already generated the CCS (consensus sequences) , I converted that ccs.bam file into a ccs.fa file . I would like to know if my command line looks great : canu -assemble -p assembly -d pacbio genomeSize=1200m -pacbio-hifi ccs.fa Do I need to ...
hicanu ccs pacbio written 8 weeks ago by pablo140
0
votes
0
answers
128
views
0
answers
Comment: C: Improving PacBio Assembly with Illumina reads
... Thanks for the tips. I'm probably gonna use Pilon to polish my assemblies with Illumina reads, in order to get 1 contig. ...
written 10 weeks ago by pablo140
0
votes
0
answers
128
views
0
answers
Improving PacBio Assembly with Illumina reads
... Hello, I had to make an assembly with PacBio reads . It is a bacterial genome (~ 4Mb ) . For some of the samples, I got 1 contig but for some others, I got 2 to 4 contigs while I would like to get only 1 contig . Could it be a solution to use Illumina reads and an hybrid assembler to polish my Pa ...
assembly pacbio illumina written 10 weeks ago by pablo140
0
votes
0
answers
198
views
0
answers
Comment: C: Get statistics about an alignment done by Hifiasm
... You're right, I edited my post. Do you have an idea about my question? ...
written 11 weeks ago by pablo140
0
votes
0
answers
198
views
0
answers
Get statistics about an alignment done by Hifiasm
... Hi , I had consensus reads (ccs.bam) from a PacBio sequencing. I used the assembler `hifiasm` to create an assembly on these CCS. I got several `.gfa` files but I would like to get some statistics on the assembly : % mapped reads , size of the assembly ... How could I do this? Thanks ...
alignment hifiasm written 11 weeks ago by pablo140
0
votes
1
answer
203
views
1
answers
Comment: C: Fastq files with only " ! " score
... Actually, I used the `bam2fastq` tool, but as I said, I also got "!" score for each base. My data are pretty new. ...
written 12 weeks ago by pablo140
2
votes
1
answer
203
views
1
answer
Fastq files with only " ! " score
... Hello, I got reads from PacBio sequencing. The reads are in BAM format. I converted them into FASTQ format. I both used the `bam2fastq` and `samtools fastq` tools to do that. The problem I have is that I got the " ! " score for all bases of the sequences with both tools, which means the bases are ...
fastq samtools written 12 weeks ago by pablo140 • updated 12 weeks ago by genomax91k

Latest awards to pablo

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Correlation Matrix - Big Data - R
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Mapping vs Quasi-Mapping
Popular Question 3 months ago, created a question with more than 1,000 views. For Correlation Matrix - Big Data - R
Popular Question 4 months ago, created a question with more than 1,000 views. For Salmon quantification vs HTSeq count quantification
Popular Question 11 months ago, created a question with more than 1,000 views. For Difference between HTSeq-count & Salmon quant results
Popular Question 14 months ago, created a question with more than 1,000 views. For Mapping vs Quasi-Mapping
Centurion 16 months ago, created 100 posts.
Popular Question 20 months ago, created a question with more than 1,000 views. For Mapping vs Quasi-Mapping

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1387 users visited in the last hour