SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.09 seconds.
Search: Posts Made By: GenoMax
Forum: Bioinformatics 01-14-2022, 06:43 PM
Replies: 2
Views: 300
Posted By GenoMax
Another variation: $ esearch -db gene...

Another variation:


$ esearch -db gene -query "PCSK9 [GENE] AND human [ORGN]" | esummary | xtract -pattern DocumentSummary -element Name,Summary
PCSK9 This gene encodes a member of the...
Forum: Bioinformatics 01-14-2022, 06:41 PM
Replies: 2
Views: 300
Posted By GenoMax
Using Entrezdirect (http://bit.ly/entrez-direct):...

Using Entrezdirect (http://bit.ly/entrez-direct):


$ esearch -db gene -query "PCSK9 [GENE] AND human [ORGN]" | efetch -format acc

1. PCSK9
Official Symbol: PCSK9 and Name: proprotein...
Forum: Bioinformatics 01-14-2022, 06:36 PM
Replies: 1
Views: 313
Posted By GenoMax
Use Entrezdirect:...

Use Entrezdirect: https://www.ncbi.nlm.nih.gov/books/NBK179288/
Forum: Bioinformatics 01-11-2022, 11:21 AM
Replies: 6
Views: 6,243
Posted By GenoMax
That numbering is odd. Versions went from 1.3,...

That numbering is odd. Versions went from 1.3, 1.4 to 1.10,1.11,1.12 etc. Currently 1.14.

See: https://github.com/samtools/samtools/releases/
Forum: Bioinformatics 01-09-2022, 05:40 AM
Replies: 6
Views: 6,243
Posted By GenoMax
@Genom: Your question has been answered in...

@Genom: Your question has been answered in https://www.biostars.org/p/9504545/#9504848
Forum: Illumina/Solexa 12-12-2021, 06:01 AM
Replies: 1
Views: 544
Posted By GenoMax
Also at: https://www.biostars.org/p/9501284/

Also at: https://www.biostars.org/p/9501284/
Forum: Illumina/Solexa 12-05-2021, 05:33 PM
Replies: 6
Views: 1,191
Posted By GenoMax
Have you had Illumina tech support a look at this...

Have you had Illumina tech support a look at this run? They can do that remotely. Sounds like there may be a hardware/software issue (assuming you have libraries that will amplify by qPCR).
Forum: Site Feedback/Suggestions 12-02-2021, 07:13 AM
Replies: 2
Views: 892
Posted By GenoMax
I think attachments may have been disallowed...

I think attachments may have been disallowed after a point in time. Edit your post and include the traces as an image.
Forum: Bioinformatics 11-30-2021, 04:36 PM
Replies: 6
Views: 1,563
Posted By GenoMax
I don't think there is a non-redundant nt...

I don't think there is a non-redundant nt database. You should consider using RefSeq/RefSeq genomes.

Perhaps the only way to put this to rest is to email NCBI help desk and ask. There is some...
Forum: Bioinformatics 11-29-2021, 02:44 PM
Replies: 6
Views: 1,563
Posted By GenoMax
If you downloaded `nr` as pre-formatted database...

If you downloaded `nr` as pre-formatted database from NCBI then it is a protein only database as noted in the blastftp file (https://ftp.ncbi.nlm.nih.gov/blast/blastftp.txt).
Forum: Bioinformatics 11-29-2021, 06:01 AM
Replies: 6
Views: 1,563
Posted By GenoMax
nr is a protein database. You are trying to use...

nr is a protein database. You are trying to use blastn with that. You will need to use blastx or a translated protein search.
Forum: Bioinformatics 10-25-2021, 06:35 AM
Replies: 4
Views: 1,356
Posted By GenoMax
If you need full length perfect alignments in...

If you need full length perfect alignments in your final file then I suggest that you try "perfectmode=t minid=1 mappedonly=t" options. If your reads are longer than 150 bp then you may need to...
Forum: Bioinformatics 10-25-2021, 05:13 AM
Replies: 4
Views: 1,356
Posted By GenoMax
Do you have 20 cores available on the machine for...

Do you have 20 cores available on the machine for BBMap to use. What happens if you assign fewer cores? Starting with 8 would be a good number.
Forum: Bioinformatics 10-15-2021, 12:40 PM
Replies: 1
Views: 1,164
Posted By GenoMax
You can align your contigs to the genome sequence...

You can align your contigs to the genome sequence and check. A program like Mauve (http://darlinglab.org/mauve/mauve.html) also comes in handy to check the coverage visually.
Forum: Bioinformatics 10-13-2021, 12:47 PM
Replies: 348
Views: 195,660
Posted By GenoMax
DP: You should use `bbsplit.sh` to do...

DP: You should use `bbsplit.sh` to do read-binning to remove host data contamination. There is a thread here that describes how to use that tool.

Use bbduk for just adapter removal. Using it in...
Forum: Bioinformatics 09-28-2021, 04:13 AM
Replies: 348
Views: 195,660
Posted By GenoMax
@lituan you will need to use k=2 or less with...

@lituan you will need to use k=2 or less with such a short pattern (CCGG). Even then it may not work well.

This may be a case where you would want to use a different package called Seqkit...
Forum: Bioinformatics 09-27-2021, 07:14 AM
Replies: 3
Views: 1,373
Posted By GenoMax
Python is generally symlinked to python v.2.x....

Python is generally symlinked to python v.2.x. Can you explicitly try `python3`?
Forum: Metagenomics 09-24-2021, 11:59 AM
Replies: 3
Views: 3,582
Posted By GenoMax
See:...

See: http://seqanswers.com/forums/showthread.php?t=41288
Forum: Bioinformatics 09-23-2021, 03:09 PM
Replies: 1
Views: 1,233
Posted By GenoMax
Is there a specific reason you converted these...

Is there a specific reason you converted these reads to fasta format? If this is data from SRA then you should be able to map the fastq reads directly.

You may be getting secondary alignments and...
Forum: Bioinformatics 09-23-2021, 03:06 PM
Replies: 699
Views: 257,540
Posted By GenoMax
You should be able to use covstats=<file> ...

You should be able to use covstats=<file> Per-scaffold coverage info. for each of your commands. You can also capture the stderr/out to a file to get statistics....
Forum: Metagenomics 09-23-2021, 03:03 PM
Replies: 3
Views: 3,582
Posted By GenoMax
You should use a different program for this...

You should use a different program for this purpose. Look up "bbsplit.sh". BBDuk is not the right program for this application.
Forum: Bioinformatics 09-21-2021, 06:24 AM
Replies: 1
Views: 1,005
Posted By GenoMax
You could use "minimap2" to align against the...

You could use "minimap2" to align against the human genome. That said you will need to be judicious about results as you determine what is "human" contamination. Depending on the genomes you are...
Forum: Bioinformatics 09-18-2021, 07:00 AM
Replies: 6
Views: 1,344
Posted By GenoMax
Brian's email address is in the inline help for...

Brian's email address is in the inline help for bbmap programs. Just run `bbmap.sh` and look through the help.

It may be by design then. Error correction requires keeping large amount of sequence...
Forum: Bioinformatics 09-17-2021, 11:58 AM
Replies: 6
Views: 1,344
Posted By GenoMax
I may have bad news. All bbmap tools are supposed...

I may have bad news. All bbmap tools are supposed to be able to accept input from STDIN but it appears that "tadpole.sh" may be an exception. This is something Brian (author of BBMap may know the...
Forum: Illumina/Solexa 09-16-2021, 03:03 PM
Replies: 2
Views: 1,453
Posted By GenoMax
NovaSeq may be an overkill unless you have...

NovaSeq may be an overkill unless you have multiple bacterial genomes you are planning to sequence at the same time. This paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706130/) is a good read...
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 11:51 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO