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Search: Posts Made By: GenoMax
Forum: Bioinformatics 05-07-2022, 03:10 AM
Replies: 2
Views: 677
Posted By GenoMax
FastQC is a quality assessment program. It does...

FastQC is a quality assessment program. It does not change any data or do actual analysis.

If you are planning to do alignments against a good reference then you don't strictly need to do any...
Forum: Bioinformatics 04-14-2022, 11:20 AM
Replies: 354
Views: 207,354
Posted By GenoMax
5g is not enough. Depending on the size of the...

5g is not enough. Depending on the size of the data you may need tens of gigs. Seal needs to keep a lot of sequences in memory and will need more of it as the size of the data increases.
Forum: Bioinformatics 04-12-2022, 10:05 AM
Replies: 354
Views: 207,354
Posted By GenoMax
Can you post the full command? Hopefully you are...

Can you post the full command? Hopefully you are explicitly asking for additional memory using -XmxNNg command
Forum: Illumina/Solexa 02-20-2022, 04:14 AM
Replies: 1
Views: 971
Posted By GenoMax
Reads are always lost to "random" indexes in...

Reads are always lost to "random" indexes in multiplexed pools. Some are sequencing/phasing errors. There is not much one can do about these. As long as you recovered expected indexes in majority of...
Forum: Bioinformatics 01-31-2022, 02:42 AM
Replies: 16
Views: 24,878
Posted By GenoMax
@Genom: As answered on Biostars you need to have...

@Genom: As answered on Biostars you need to have all command line options on one line. If command needs to span multiple lines then a \ is needed at the end of incomplete lines.
Forum: Bioinformatics 01-14-2022, 05:43 PM
Replies: 3
Views: 1,428
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, 05:41 PM
Replies: 3
Views: 1,428
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, 05:36 PM
Replies: 1
Views: 962
Posted By GenoMax
Use Entrezdirect:...

Use Entrezdirect: https://www.ncbi.nlm.nih.gov/books/NBK179288/
Forum: Bioinformatics 01-11-2022, 10:21 AM
Replies: 6
Views: 7,163
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, 04:40 AM
Replies: 6
Views: 7,163
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, 05:01 AM
Replies: 1
Views: 1,342
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, 04:33 PM
Replies: 6
Views: 2,230
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, 06:13 AM
Replies: 2
Views: 3,336
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, 03:36 PM
Replies: 6
Views: 1,986
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, 01:44 PM
Replies: 6
Views: 1,986
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, 05:01 AM
Replies: 6
Views: 1,986
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, 05:35 AM
Replies: 4
Views: 1,778
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, 04:13 AM
Replies: 4
Views: 1,778
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, 11:40 AM
Replies: 1
Views: 1,387
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, 11:47 AM
Replies: 354
Views: 207,354
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, 03:13 AM
Replies: 354
Views: 207,354
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, 06:14 AM
Replies: 3
Views: 1,886
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, 10:59 AM
Replies: 3
Views: 7,819
Posted By GenoMax
See:...

See: http://seqanswers.com/forums/showthread.php?t=41288
Forum: Bioinformatics 09-23-2021, 02:09 PM
Replies: 1
Views: 1,565
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, 02:06 PM
Replies: 703
Views: 271,532
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....
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