Moderator: shenwei356
shenwei356 ♦ 4.4k
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Posts by shenwei356
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3
answers
160
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3
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... Just use `seqkit seq -n -i seqs.fa ` to retrieve IDs. ...
written 5 days ago by
shenwei356 ♦ 4.4k
1
vote
2
answers
4.0k
views
2
answers
... [BLAST+ 2.8.1 with blastdb v5](https://ncbiinsights.ncbi.nlm.nih.gov/2019/01/04/blast-2-8-1-with-new-databases-and-better-performance/) allow you to limit your search by taxonomy using information built into the BLAST databases. So you don't need to build blastdb for specific taxids now ! ...
written 10 days ago by
shenwei356 ♦ 4.4k
0
votes
2
answers
107
views
2
answers
... Try [`seqkit grep`](https://bioinf.shenwei.me/seqkit/download/) ([usage](https://bioinf.shenwei.me/seqkit/usage/#grep)).
seqkit grep -i -s -r -p '[zxb]' -v
# cat test.fa | seqkit grep --ignore-case --by-seq --use-regexp --pattern '[zxb]' --invert-match
# seqkit grep -i -s -p z -p ...
written 13 days ago by
shenwei356 ♦ 4.4k
1
vote
2
answers
107
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2
answers
... Will you remove sequences containing `J`?
```
A Ala Alanine
B Asx Aspartic acid or Asparagine [2]
C Cys Cysteine
D Asp Aspartic Acid
E Glu Glutamic Acid
F Phe Phenylalanine
G Gly Glycine
H His Histidine
I Ile Isoleucine
J Isoleucine or Leucine [4]
K Lys Lysine
L Leu Leucine
M Met Meth ...
written 13 days ago by
shenwei356 ♦ 4.4k
0
votes
1
answer
286
views
1
answers
Comment:
C: Designing a primer from reads
... As you tagged, you should assemble the genome or target sequence region firstly, before designing primers.
Actually, I have no idea about what you want.
...
written 13 days ago by
shenwei356 ♦ 4.4k
0
votes
0
answers
102
views
0
answers
... It seems like a homework, or [XY Problem](http://xyproblem.info/). You should at least tell us what have you tried, or why do you want to this, what's the original purpose. ...
written 13 days ago by
shenwei356 ♦ 4.4k
0
votes
2
answers
302
views
2
answers
... I can send nr.3041.fa.gz (70M) to you via email, if you give my address or write email to me.
...
written 24 days ago by
shenwei356 ♦ 4.4k
0
votes
2
answers
302
views
2
answers
... Well, I tried 3041, and every step worked fine.
$ wc -l $id.taxid.txt
9703 3041.taxid.txt
$ wc -l $id.acc.txt
383332 3041.acc.txt
$ pigz -dc nr.$id.fa.gz | grep '^>' -c
383332
$ time makeblastdb -parse_seqids -in nr.$id.fa -dbtype prot -out nr.$id
Building a ne ...
written 24 days ago by
shenwei356 ♦ 4.4k
0
votes
1
answer
266
views
1
answers
... checking is id2head.tsv blank.
if it is, paste result of
seqkit seq -n df1.fa | head -n 5 | cat -A
if not, paste result of
head -n 5 id2head.tsv | cat -A
...
written 24 days ago by
shenwei356 ♦ 4.4k
0
votes
2
answers
302
views
2
answers
... please paste results of
wc -l 3041.taxid.txt
wc -l 3041.acc.txt
I'll check it on monday.
...
written 25 days ago by
shenwei356 ♦ 4.4k
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