User: cedric.laczny

gravatar for cedric.laczny
Reputation:
50
Status:
New User
Location:
Germany
Twitter:
@claczny
Last seen:
1 year ago
Joined:
4 years, 10 months ago
Email:
c************@gmail.com

Posts by cedric.laczny

<prev • 7 results • page 1 of 1 • next >
0
votes
2
answers
2.0k
views
2
answers
Answer: A: run BLASTn remotly
... Since previous posts posted about where the problem likely comes from, here is a post providing at least some direction to resolve the issue: https://www.biostars.org/p/177185/ At least, that worked for me after getting the respective information, i.e., the HTTP_PROXY_HOST and HTTP_PROXY_PORT which ...
written 2.1 years ago by cedric.laczny50
2
votes
3
answers
5.5k
views
3
answers
Comment: C: How do I access genome coverage using SPADES?
... I am not 100% sure, but I think this is the *k-mer* coverage and *not* the read coverage. S.a. https://www.biostars.org/p/221672/ and http://seqanswers.com/forums/showthread.php?t=6887 ...
written 2.3 years ago by cedric.laczny50
0
votes
4
answers
6.9k
views
4
answers
Answer: A: Fastx_Collapser Has No Fastq Output
... Albeit this is an old post, maybe some other will find this useful too: http://seqcluster.readthedocs.io/collapse.html N.B. That it requires quite a few python dependencies, which, just as `seqcluster` itself, can be installed via `pip`. [UPDATE] The code described at https://www.biostars.org/p/27 ...
written 3.0 years ago by cedric.laczny50
2
votes
1
answer
766
views
1
answers
Comment: C: Optimizing sample extraction and concatenation from vcf files
... +1 for using `make`. My suggestion using pattern rules: SHELL=/bin/bash INPUT=your.input.vcf.gz SAMPLES=$(shell gunzip -c ${INPUT}| grep -m1 '\#CHROM' | cut -f 10- ) all: $(foreach S,${SAMPLES}, ${S}/${S}.vcf.gz) %.vcf.gz: $(INPUT) mkdir -p $(dir $@) ...
written 3.1 years ago by cedric.laczny50
0
votes
1
answer
4.3k
views
1
answers
Comment: C: SRAtoolkit error during fastq-dump
... Thx! Upvoted. On that note, I just stumbled over http://ncbi.github.io/sra-tools/install_config.html -> vdb-config provides a "graphical" configuration screen. N.B. As indicated by @piet, do *not* use "http://" in front of the proxy as it won't work then (at least it didn't in my case). ...
written 3.2 years ago by cedric.laczny50
1
vote
3
answers
20k
views
3
answers
Comment: C: Scientific Names In Blast Output And Databases
... FWIW, I had to use: tar -xzf taxdb.tar.gz ...
written 4.1 years ago by cedric.laczny50 • updated 11 months ago by h.mon27k
0
votes
3
answers
4.5k
views
3
answers
Comment: C: What are the best approaches to evaluate a genome assembly using the 'intrinsic'
... Don't (yet) know about the other two, but FRCbam needs actually _two_ libraries, a paired-end (PE) library and a mate-paired (MP) library. It seems that the original poster only has a PE-library. Don't know if there are then any "hacks" to get FRCbam to work correctly on such data. ...
written 4.8 years ago by cedric.laczny50

Latest awards to cedric.laczny

Supporter 4.0 years 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: 2113 users visited in the last hour