User: treitlis

gravatar for treitlis
treitlis30
Reputation:
30
Status:
New User
Location:
Last seen:
3 months, 4 weeks ago
Joined:
2 years, 12 months ago
Email:
t*******@natur.cuni.cz

Posts by treitlis

<prev • 14 results • page 1 of 2 • next >
0
votes
0
answers
303
views
0
answers
Comment: C: Pilon polishing highly repetitive nanopore assembly
... Thank you for your quick reply. The chloroplast genome is probably 500 kbp (I am not sure even now, because I have also nuclear, and bacterial data in the dataset). I have two main contigs one which is 240 kbp and one which is 160 kbp and some other smaller ones for the canu assembly. The number o ...
written 4 months ago by treitlis30
2
votes
0
answers
303
views
0
answers
Pilon polishing highly repetitive nanopore assembly
... Hi all, I would like to ask you for some suggestions for pilon polishing of a canu assembled genome. Long story short, we try to assemble a chloroplast genome which is extremely repetitive. We have around 3Gbp of nanopore data, and we are unable to make a single contig from the genome Before we tr ...
genome assembly pilon nanopore canu written 4 months ago by treitlis30 • updated 4 months ago by WouterDeCoster38k
0
votes
5
answers
1.5k
views
5
answers
Answer: A: Local blast custom databases
... Hello, Thank you for your replies. Deconseq kinda works and kinda not. It's not the best tool for my job. I don't have reference for the contaminants (they are unsequenced bacteria) but I have some close relatives in NCBI. Deconseq removes kinda 4-5% of the reads which obliviously it's not correct ...
written 2.1 years ago by treitlis30
0
votes
5
answers
1.5k
views
5
answers
Comment: C: Local blast custom databases
... Sorry for the late rely. Thank you for the information, but I don't know how well this version will help me. However, as I saw there is still possibility to use the GI numbers, and even now you can still download the GI list. I will try to use eutils to download the accession list and use seqid as ...
written 2.5 years ago by treitlis30
0
votes
5
answers
1.5k
views
5
answers
Comment: C: Local blast custom databases
... Hello, I don't know what's with NCBI but to download the accession list for a group it will take ages. I don't know why the download of the accession list goes with max 1 kb/s but I am able to download the gilist with 250kb/s and if I try to download all sequences as fasta for a group I can downloa ...
written 2.6 years ago by treitlis30
0
votes
5
answers
1.5k
views
5
answers
Comment: C: Local blast custom databases
... Hello, Good example in your paper, but my case is very different. I don't want to enter in detail why I chosen this path. Even [prodege][1], with it's very complex algorithm is unable to decontaminate the data. Also in FastQC I see a nice clear peak of GC content, not two peaks, or more, and in my ...
written 2.6 years ago by treitlis30
0
votes
5
answers
1.5k
views
5
answers
Comment: C: Local blast custom databases
... Hello, I think I completely missed this parameter of the blast. I will try to download the accession number for some organism and try if to see how it will work and post back. Anyway thank you very much for pointing out this parameter. ...
written 2.6 years ago by treitlis30
0
votes
5
answers
1.5k
views
5
answers
Comment: C: Local blast custom databases
... Hello, I know those tools, but they are not helpful when you are not working on well known organisms, or when the contaminants are not present in the nt database. I still use the tools to generate the plot before and after, but they are not well suited for my needs. ...
written 2.6 years ago by treitlis30
1
vote
5
answers
1.5k
views
5
answers
Local blast custom databases
... Hi, I work on some protist genomes and because the protists live in symbiosis with bacteria usually I have bacterial contamination in the NGS data. Previously, I was using a script to decontaminate the genomic data from bacterial hits, and among other things, the script was based on blastn and bla ...
ncbi gi numbers gilist written 2.6 years ago by treitlis30
0
votes
0
answers
1.7k
views
0
answers
Comment: C: SPAdes insert size
... Hi there, Thank you very much. It was such a stupid mistake from my side. On our server wikipage the libraries were marked paired-end. Unfortunately the library was prepared by the sequencing company and the person who took the data an put it on the webpage annotated it in the wrong way. Thank yo ...
written 2.6 years ago by treitlis30

Latest awards to treitlis

Popular Question 23 months ago, created a question with more than 1,000 views. For Remove contaminant reads using Bowtie2
Popular Question 23 months ago, created a question with more than 1,000 views. For Local blast custom databases
Popular Question 23 months ago, created a question with more than 1,000 views. For SPAdes insert size

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1084 users visited in the last hour