User: zhangdengwei
zhangdengwei • 50
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Posts by zhangdengwei
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... 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 ...
written 5 days ago by
zhangdengwei • 50
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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
zhangdengwei • 50
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... 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 ...
written 11 days ago by
zhangdengwei • 50
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C: how to merge two big file faster
... metaphlan2 and humann2 ...
written 11 days ago by
zhangdengwei • 50
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C: how to merge two big file faster
... Thanks very much. Your comment is pretty helpful to me. ...
written 11 days ago by
zhangdengwei • 50
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C: how to merge two big file faster
... Thanks for your advice. ...
written 11 days ago by
zhangdengwei • 50
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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
zhangdengwei • 50
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... 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! ...
written 12 days ago by
zhangdengwei • 50
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... Thanks. I found `Mugsy` was competent for this. I will try to use `Mauve` later. ...
written 10 weeks ago by
zhangdengwei • 50
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... 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!!! ...
written 10 weeks ago by
zhangdengwei • 50
• updated
10 weeks ago by
onestop_data • 190
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