User: gtrwst9

gravatar for gtrwst9
gtrwst90
Reputation:
0
Status:
New User
Last seen:
20 hours ago
Joined:
7 months, 3 weeks ago
Email:
g******@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by gtrwst9

<prev • 16 results • page 1 of 2 • next >
0
votes
1
answer
73
views
1
answers
Comment: C: Complete phylogenetic trees?
... Thanks both. Acually ITOL provides complete trees in newick, nexus and phyloxml format so, presumably, also the distances. But their example tree has only a few hundred nodes. ...
written 23 hours ago by gtrwst90
1
vote
1
answer
73
views
1
answer
Complete phylogenetic trees?
... Hello, where can I get trees with distance information of whole classes or kingdoms like bacteria? Someone must have done this already for the known genomes. Please note, distances must be included, else it would just be a taxonomic tree. ...
phylogenetic tree of life taxonomy tree written 1 day ago by gtrwst90
1
vote
1
answer
264
views
1
answer
Fosmid contamination in C. elegans genome?
... In the C. elegans chromosome X (NC_003284.9) is a complete copy of the C. elegans fosmid H05L03 (FO081428.1) at positions 5898291-5912640. I understand fosmids are vectors used to build sequencing libraries, so is this a contamination? ...
genome written 5 months ago by gtrwst90 • updated 5 months ago by Ahill1.4k
3
votes
1
answer
317
views
1
answer
command-line tool to split genome FASTA into equal chunks?
... Say I have the file for accession LS483306.1 which is one big sequence starting with >LS483306.1 xyz AGCT... and want to have one file with N sequences of size X, looking like this (example X=2000): >LS483306.1:1-2000 xyz AGCT... >LS483306.1:2001-4000 xyz GCTA... ...
software fasta conversion written 6 months ago by gtrwst90 • updated 6 months ago by genomax63k
0
votes
2
answers
675
views
2
answers
Answer: A: Problem in processing SRA file from NCBI
... `fastq-dump --split-3 SRR...` This does NOT redownload everything. ...
written 6 months ago by gtrwst90
0
votes
2
answers
908
views
2
answers
Answer: A: convert SRA file into forward and reverse fastq files
... `fastq-dump --split-3 SRR...` This does NOT redownload everything. ...
written 6 months ago by gtrwst90
0
votes
0
answers
5.0k
views
0
answers
Comment: C: linux 'cat' command merge fasta files without headers
... Probably the dash was surrounded by spaces. If you have filenames with spaces enclose the name with single or double quotes like `cat "Escherichia coli - genome.fa"`. ...
written 6 months ago by gtrwst90
0
votes
1
answer
138
views
1
answers
Answer: A: Taxa lists from Human Microbiome Project?
... Found it. This page lists the datasets grouped according to body sites: https://www.hmpdacc.org/hmp/HMASM/ and on this page: https://www.hmpdacc.org/hmp/HMSCP/ you can then download the abundance tables. Unfortunately skin sites are only one, the retroauricular. So my problem remains, although the ...
written 6 months ago by gtrwst90
0
votes
1
answer
138
views
1
answer
Taxa lists from Human Microbiome Project?
... Has anyone attempted to generate a list of taxa (at spec. body site), even without abundancies? This should be possible with the WGS part of the data, as 16S is too error prone. I would be very interested in having a list of the skin, esp. of the back. But a complete (as in all sites) list would be ...
hmp metagenomic written 6 months ago by gtrwst90
0
votes
1
answer
248
views
1
answers
Comment: C: number of matching bases in set of sequences aligning with one genome
... Many thanks. I was thinking in too exact terms, but it's all about probability so Mash and the returned p-value suits me fine. ...
written 6 months ago by gtrwst90

Latest awards to gtrwst9

Scholar 22 hours ago, created an answer that has been accepted. For A: Complete phylogenetic trees?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1052 users visited in the last hour