Moderator: shenwei356
shenwei356 ♦ 4.7k
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Posts by shenwei356
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3
votes
2
answers
140
views
2
answers
... ```
# IDs in seqs.fa
$ grep '^>' seqs.fa | awk '{print $1}' | sed 's/^>//'
M.Bce12308ORF4755P
M.Bce1254ORF9725P
# IDs not in list.txt
$ grep -w -v -f <(grep '^>' seqs.fa | awk '{print $1}' | sed 's/^>//') list.txt
M.Bce122ORF1082P
``` ...
written 19 days ago by
shenwei356 ♦ 4.7k
6
votes
1
answer
184
views
1
answers
Answer:
C: Kill nohup bash process
... Hi, I'd recommend using [screen](https://linuxize.com/post/how-to-use-linux-screen/) instead of `nohup`, screen is safer.
And, you better utilize some batch commands like `parallel` to accelerate thousands of jobs, here is `wget`.
Using `wget -c` to resume unfinished download is also recommended. ...
written 5 weeks ago by
shenwei356 ♦ 4.7k
1
vote
1
answer
196
views
1
answers
... Use [seqkit](https://github.com/shenwei356/seqkit) for saving time.
seqkit stats xxxx_R[12].*.fastq.gz
Results are something like these:
```
$ seqkit stats reads_*.fq.gz
file format type num_seqs sum_len min_len avg_len max_len
reads_1.fq.gz FASTQ DNA 2,500 567,516 ...
written 3 months ago by
shenwei356 ♦ 4.7k
0
votes
0
answers
224
views
0
answers
... Just for given sample data.
```
$ sed 's/^>//' headers.txt | perl -pne 's/(\w+_\w+)_/$1\t/' > headers.tsv
$ cat headers.tsv
NZ_CP023010 Elizabethkingia anophelis FDAARGOS_198
NZ_MRWY01000004 Klebsiella michiganensis_CAV1755
$ seqkit replace -p '^(.+?)\..+_' -k headers.tsv -r '{kv}_' ...
written 3 months ago by
shenwei356 ♦ 4.7k
1
vote
1
answer
333
views
1
answers
... ```
$ spades.py --help
SPAdes genome assembler v3.13.0
...
Advanced options:
--dataset file with dataset description in YAML format
-t/--threads number of threads
[default: 16]
-m/--memory RAM limit for SPAdes in Gb (terminat ...
written 4 months ago by
shenwei356 ♦ 4.7k
0
votes
2
answers
264
views
2
answers
... Yes I know, I guess proteins of bacteria in RefSeq are enough for his/her purpose, before knowing for what he/she use the data.
Anyway, one can try
```
# downlaod
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt
# reformat
cat assembly_summary.txt | sed 1d | sed '1s/^# ...
written 4 months ago by
shenwei356 ♦ 4.7k
0
votes
2
answers
264
views
2
answers
... You can also download `.faa.gz` files for every bacterium in [RefSeq](ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria), check [another tutorial](http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/) ...
written 4 months ago by
shenwei356 ♦ 4.7k
0
votes
2
answers
421
views
2
answers
Comment:
C: Linearize fasta files
... （￣ へ￣ ）Yes, the [patch](https://github.com/lh3/seqtk/pull/123) is worth it. Thank you Fabian for this great patch! ...
written 5 months ago by
shenwei356 ♦ 4.7k
2
votes
2
answers
421
views
2
answers
Answer:
C: Linearize fasta files
... `seqtk seq input.fa` (1.3-r106 [68752fd](https://github.com/lh3/seqtk/commit/68752fd8497aff82b273b1f7f541b9905760586f)) is faster than `seqkit seq -w 0 input.fa` (v0.10.0) in my test on both SSD and HDD.
Version:
- seqkit [v0.10.0](https://github.com/shenwei356/seqkit/releases/tag/v0.10.0)
- seqtk ...
written 5 months ago by
shenwei356 ♦ 4.7k
1
vote
2
answers
394
views
2
answers
... [seqkit subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) supports this, if you want a fast solution.
seqkit subseq -r -1000:-1 seqs.fa > result.fa
If you want to learn programming, write some Python scripts using Biopython. ...
written 5 months ago by
shenwei356 ♦ 4.7k
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