Moderator: shenwei356
shenwei356 ♦ 4.1k
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Posts by shenwei356
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... (Only for full match)
```
# positive strand
$ cat seqs.fa | seqkit grep -s -d -p NACTGN | seqkit seq -n -i | tee 1.txt
Contig4679
Contig4682
# negative strand
$ cat seqs.fa | seqkit seq -r -p | seqkit grep -s -d -p TTAM | seqkit seq -n -i | tee 2.txt
Contig4681
Contig4682
# intersection
$ csvtk i ...
written 8 days ago by
shenwei356 ♦ 4.1k
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... Partly match between PCR primer and target sequence is enough for PCR amplication. Do you still want only full match? ...
written 8 days ago by
shenwei356 ♦ 4.1k
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103
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... why not trying googling using keywords "r dataframe reorder factor"? ...
written 8 days ago by
shenwei356 ♦ 4.1k
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... In R, just set the column as factor with your levels for the dataframe.
For others, storing the levels in a hashmap with incremental numbers as values, then you can sort the rows using corresponding hashmap value.
Want save time? [csvtk sort](https://bioinf.shenwei.me/csvtk/usage/#sort) supports s ...
written 8 days ago by
shenwei356 ♦ 4.1k
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... finally, there's no bug and sequences count matches (Here 6928017 ~= 6928021). ...
written 9 days ago by
shenwei356 ♦ 4.1k
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... test: blastp
# blastdb from step 3 option 2
#
time blastp -num_threads 16 -db nr.$id -query t4.fa > t4.fa.blast
# real 0m20.866s
# $ cat t4.fa.blast | grep Query= -A 10
# Query= A0A0J9X1W9.2 RecName: Full=Mu-theraphotoxin-Hd1a; Short=Mu-TRTX-Hd1a
#
# ...
written 9 days ago by
shenwei356 ♦ 4.1k
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... Data:
- [pre-formated blastdb](ftp://ftp.ncbi.nlm.nih.gov/blast/db) (09/10/2018)
- [prot.accession2taxid.gz](ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz) (09/07/2018) (optional, but recommended)
Hardware in this tutorial
- CPU: AMD 8-cores/16-threads 3.7Ghz
- RAM: ...
written 9 days ago by
shenwei356 ♦ 4.1k
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... Sorry for this bug. I've downloaded the nr and rewrite the steps posted as a new answer. There's no bug now. ...
written 9 days ago by
shenwei356 ♦ 4.1k
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231
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... buggy means failing to retrieve some sequences, makeblastdb works fine.
option a is ouputtin from pre-built blastdb downloaded from ftp. ...
written 10 days ago by
shenwei356 ♦ 4.1k
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... It's the bug of the perl one-liner, because of the not well formated `nr.gz`.
I gave up after few hours. May be we should blast on whole `nr` and filter the result. ...
written 10 days ago by
shenwei356 ♦ 4.1k
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