User: hcwang

gravatar for hcwang
hcwang50
Reputation:
50
Status:
New User
Location:
Vancouver, Canada
Last seen:
11 months, 2 weeks ago
Joined:
3 years, 3 months ago
Email:
w*************@hotmail.com

Posts by hcwang

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Is it possible to automatically update NCBI fasta sequences in command-line?
... Thank you for all your responses! To add into @genomax2 's question, I'm building local copies of all virus, bacteria, and fungi databases for detection of organisms from Illumina sequencing runs using local blast and RAPSearch2. Minor versions are alright but some of the removed sequences really al ...
written 3.3 years ago by hcwang50
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Is it possible to automatically update NCBI fasta sequences in command-line?
... Hi all, I downloaded fasta sequences from NCBI FTP site with the method described in http://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#allcomplete . Recently, I used my customised database for blast and got many desired results. However, one thing I noticed is that some of the sequences have been upd ...
ncbi fasta update command-line written 3.3 years ago by hcwang50 • updated 3.3 years ago by Matt Shirley9.1k
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Comment: C: Retrieve a subset of FASTA from large multi-FASTA file
... Thanks for the information! In fact, I tried almost all of the methods these threads provided. It might be because I'm not used to using other tools. samtools faidx took many hours to retrieve 10,000 fasta records from a 40M read file. Biopython simply took forever to load the 40M read file. So, I c ...
written 3.3 years ago by hcwang50
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Comment: C: Retrieve a subset of FASTA from large multi-FASTA file
... Does this one work with retrieval based on Query FASTA IDs? For example, I have a long list of query IDs from a Illumina sequencing file, does BBMap efficiently retrieve a subset of the Illumina read FASTA? ...
written 3.3 years ago by hcwang50
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Comment: C: Retrieve a subset of FASTA from large multi-FASTA file
... Please comment on the efficiency of this program. Also, it seems like this one requires GI/Accession IDs to work. Does it work if I have a long list of query IDs? Thank you for your input! ...
written 3.3 years ago by hcwang50
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Comment: C: Retrieve a subset of FASTA from large multi-FASTA file
... Thank you for the reply! I wish I found this answer before so I can avoid hitting so many walls. ...
written 3.3 years ago by hcwang50
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Comment: C: Retrieve a subset of FASTA from large multi-FASTA file
... I agree with you. I wrote my script only because I'm trying to get quick results with very limited memory resource. I believe the memory footprint for extracting reads in step 2 and 3 are very minimum (which is the key to the success of my run). The converted_fasta in step 1 of my script takes abo ...
written 3.3 years ago by hcwang50
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Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
... Over the past few days, I've tried many methods to extract subset of FASTA from a multi-FASTA file based on the header IDs. I've tried samtools, hpcgridrunner, biopython and various other fasta extractor tools. However, none of them worked very well or very efficiently. Using samtools, it took me da ...
fasta tool large file retrieval illumina multi-fasta written 3.3 years ago by hcwang50 • updated 3.3 years ago by shenwei3564.8k

Latest awards to hcwang

Appreciated 2.7 years ago, created a post with more than 5 votes. For Retrieve a subset of FASTA from large Illumina multi-FASTA file
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Retrieve a subset of FASTA from large Illumina multi-FASTA file

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