User: zhangdengwei

gravatar for zhangdengwei
zhangdengwei50
Reputation:
50
Status:
Trusted
Location:
Last seen:
3 days, 4 hours ago
Joined:
1 year ago
Email:
z***********@genomics.cn

Posts by zhangdengwei

<prev • 50 results • page 1 of 5 • next >
0
votes
0
answers
85
views
0
answers
how to calculate Chao 1 with the input of relative abundance of microbiota
... Dear all, I have profiled the microbial community using `metaphlan v3`, and the output was the relative abundance for each bacteria, that is, the proportion. Then I'd like to evaluate its richness with `Chao 1`, but the input for calculating `Chao 1` must be integers. Besides, the formula for calc ...
shannon chao 1 microbiota metaphlan written 5 days ago by zhangdengwei50
0
votes
0
answers
106
views
0
answers
Comment: C: how to merge two big file faster
... Indeed, the recommendation of `humann2` is the merged file. I'm not clear about the difference using one or two reads, does it impact the result? Have you tested it? ...
written 10 days ago by zhangdengwei50
0
votes
0
answers
67
views
0
answers
adopt last KEGG database to do pathway enrichment in humman2
... hi all, I'm dealing with the metagenomic data using `humann2`, to perform pathway enrichment. And the default database is `metaCyc` for pathway enrichment in `humann2`. According to its official [tutorial](https://bitbucket.org/biobakery/humann/wiki/Home#markdown-header-humann2_humann1_kegg), only ...
humann2 kegg written 11 days ago by zhangdengwei50
0
votes
0
answers
106
views
0
answers
Comment: C: how to merge two big file faster
... metaphlan2 and humann2 ...
written 11 days ago by zhangdengwei50
0
votes
0
answers
106
views
0
answers
Comment: C: how to merge two big file faster
... Thanks very much. Your comment is pretty helpful to me. ...
written 11 days ago by zhangdengwei50
0
votes
0
answers
106
views
0
answers
Comment: C: how to merge two big file faster
... Thanks for your advice. ...
written 11 days ago by zhangdengwei50
0
votes
0
answers
106
views
0
answers
Comment: C: how to merge two big file faster
... Thanks. Maybe the cause is indeed insufficient I/O. The other processes nearly run out of the I/O. I naively suppose that `cat` only consumes little CPU and ignore this case. I will try it again, with shutting down other processes. ...
written 11 days ago by zhangdengwei50
3
votes
0
answers
106
views
0
answers
how to merge two big file faster
... Hi, all I am merging two fastq files, either of which is more than 10 GB, into one file. I use `cat` to realize it, but this process took a long time, even more than 3 hours. Is there any approach to speed up it? BTW, my command is ``` cat read1.fq read2.fq > merged.fq ``` Thanks in advance! ...
cat shell written 12 days ago by zhangdengwei50
1
vote
1
answer
121
views
1
answers
Comment: C: how to find the conserved region in two or more genomes
... Thanks. I found `Mugsy` was competent for this. I will try to use `Mauve` later. ...
written 10 weeks ago by zhangdengwei50
2
votes
1
answer
121
views
1
answer
how to find the conserved region in two or more genomes
... Dear all, I'd like to find the conserved region in several genomes with FASTA format, what is the best way to pull off it? Thanks in advance!!! ...
genome fasta written 10 weeks ago by zhangdengwei50 • updated 10 weeks ago by onestop_data190

Latest awards to zhangdengwei

Popular Question 4 months ago, created a question with more than 1,000 views. For how to fix the error - Too many open files - by changing code in python3.7

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2026 users visited in the last hour