Moderator: shenwei356

gravatar for shenwei356
shenwei3564.2k
Reputation:
4,220
Status:
Trusted
Location:
China
Website:
http://shenwei.me/
Twitter:
shenwei356
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
6 years, 7 months ago
Email:
s*********@gmail.com

Posts by shenwei356

<prev • 493 results • page 2 of 50 • next >
0
votes
0
answers
209
views
0
answers
Comment: C: How to identify contigs containing the degenerate primer sequences using python?
... Partly match between PCR primer and target sequence is enough for PCR amplication. Do you still want only full match? ...
written 9 weeks ago by shenwei3564.2k
0
votes
0
answers
172
views
0
answers
Comment: C: how to reorder lines in afile based on a list of gene IDS?
... why not trying googling using keywords "r dataframe reorder factor"? ...
written 9 weeks ago by shenwei3564.2k
1
vote
0
answers
172
views
0
answers
Comment: C: how to reorder lines in afile based on a list of gene IDS?
... 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 9 weeks ago by shenwei3564.2k
0
votes
2
answers
364
views
2
answers
Comment: C: Custom nr database with only arthropods ?
... finally, there's no bug and sequences count matches (Here 6928017 ~= 6928021). ...
written 9 weeks ago by shenwei3564.2k
0
votes
2
answers
364
views
2
answers
Comment: C: Custom nr database with only arthropods ?
... 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 weeks ago by shenwei3564.2k
3
votes
2
answers
364
views
2
answers
Answer: A: Custom nr database with only arthropods ?
... 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 weeks ago by shenwei3564.2k
0
votes
2
answers
364
views
2
answers
Comment: C: Custom nr database with only arthropods ?
... 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 weeks ago by shenwei3564.2k
0
votes
2
answers
364
views
2
answers
Comment: C: Custom nr database with only arthropods ?
... buggy means failing to retrieve some sequences, makeblastdb works fine. option a is ouputtin from pre-built blastdb downloaded from ftp. ...
written 9 weeks ago by shenwei3564.2k
0
votes
2
answers
364
views
2
answers
Comment: C: Custom nr database with only arthropods ?
... 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 weeks ago by shenwei3564.2k
1
vote
2
answers
364
views
2
answers
Answer: A: Custom nr database with only arthropods ?
... ***Do not follow this answer.*** Here's the whole commands (replacing `pigz` with `gzip` if `pigz` not installed). id=6656 # Step 1) list all taxid below $id taxonkit list --ids $id --indent "" > $id.taxid.txt # Step 2) get all accessions # 3 min for me ...
written 10 weeks ago by shenwei3564.2k • updated 9 weeks ago by genomax58k

Latest awards to shenwei356

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 25 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 4 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Appreciated 4 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Appreciated 4 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 4 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 4 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 6 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 6 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 6 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 9 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1478 users visited in the last hour