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Forum: Bioinformatics 07-13-2019, 07:30 AM
Replies: 7
Views: 281
Posted By GenoMax
@SDPA_Pet: Your sequencing facility may have...

@SDPA_Pet: Your sequencing facility may have simply run 2x150 sequencing by mistake if you are sure the reads have not been trimmed.

You should be able to ask them to re-sequence the sample 2x300,...
Forum: Bioinformatics 07-12-2019, 03:24 AM
Replies: 7
Views: 281
Posted By GenoMax
What does that mean? Is the data pretrimmed,...

What does that mean? Is the data pretrimmed, which is why you have much shorter reads than expected? If all reads are 150 bp, sequencing facility may have made an error with run setup, if you had...
Forum: General 07-11-2019, 04:25 AM
Replies: 2
Views: 184
Posted By GenoMax
Do you know about 10x genomics technology? ...

Do you know about 10x genomics technology? https://www.10xgenomics.com/technology/
This may be a good topic to read up on and present.

stLFR is also similar/interesting tech. See this paper ...
Forum: Bioinformatics 07-10-2019, 03:40 AM
Replies: 235
Views: 77,589
Posted By GenoMax
Unfortunately Brian would be the only person who...

Unfortunately Brian would be the only person who can provide an authoritative answer and he no longer participates on this forum. You may want to try emailing him with your question directly.
...
Forum: Bioinformatics 07-09-2019, 09:52 AM
Replies: 235
Views: 77,589
Posted By GenoMax
Metagenome option is supposed to take in multiple...

Metagenome option is supposed to take in multiple (genome) sequences to generate an artificial metagenomic dataset.

BBMap writes stats to STDERR by default. So you can capture that.
Forum: Bioinformatics 07-09-2019, 03:25 AM
Replies: 235
Views: 77,589
Posted By GenoMax
Since you asked for 30K reads you got 30K...

Since you asked for 30K reads you got 30K paired-end reads.

I would sugegst trying without the metagenome=t option for a single small input fasta. If you do have the entire genome then use that in...
Forum: RNA Sequencing 07-08-2019, 04:02 AM
Replies: 1
Views: 128
Posted By GenoMax
Technical replicates can be merged for downstream...

Technical replicates can be merged for downstream analysis. Only biological replicates are useful for meaningful statistical analysis.
Forum: Illumina/Solexa 07-02-2019, 03:01 AM
Replies: 1
Views: 266
Posted By GenoMax
If you only plan to do one or two runs a month it...

If you only plan to do one or two runs a month it may not be worth your time. Sequencers have fine capillaries, complex electronics and are generally happier when run reasonably continuously. The...
Forum: Bioinformatics 06-26-2019, 06:32 AM
Replies: 235
Views: 77,589
Posted By GenoMax
@Noobie: I don't think so. You will have to do...

@Noobie: I don't think so. You will have to do them independently. What is the use case here, if I may ask?
Forum: Bioinformatics 06-21-2019, 10:05 AM
Replies: 2
Views: 367
Posted By GenoMax
Cross posted and answered on Biostars:...

Cross posted and answered on Biostars: https://www.biostars.org/p/385930/
Forum: Bioinformatics 06-18-2019, 05:44 AM
Replies: 6
Views: 376
Posted By GenoMax
The problem is there is no formal definition of...

The problem is there is no formal definition of fasta header. It can be anything following a ">" sign and that is what makes this problemmatic.

BBMap is actually being very flexible by allowing...
Forum: Bioinformatics 06-17-2019, 11:57 AM
Replies: 6
Views: 376
Posted By GenoMax
Since you have those numbers duplicated in your...

Since you have those numbers duplicated in your reference file fasta headers those are showing up in your alignments. BBMap is one of few aligners that passes along the entire string (including...
Forum: Bioinformatics 06-17-2019, 09:41 AM
Replies: 6
Views: 376
Posted By GenoMax
Show us the headers in your reference file. grep...

Show us the headers in your reference file. grep "^>" your_ref.fa

BTW: I don't see a "path=" or "ref=" directive in your map command above.
Forum: Bioinformatics 06-15-2019, 04:32 PM
Replies: 5
Views: 552
Posted By GenoMax
Possibly. You will have to play with parameters...

Possibly. You will have to play with parameters for bbduk.sh. "0" should be easy to get.
Forum: Bioinformatics 06-13-2019, 08:16 AM
Replies: 235
Views: 77,589
Posted By GenoMax
Have you tried adding...

Have you tried adding "VALIDATION_STRINGENCY=LENIENT" to your picard command? Default value is STRICT and sometime it leads to picard throwing errors like this.

It does looks like reformat.sh took...
Forum: Bioinformatics 06-13-2019, 02:42 AM
Replies: 5
Views: 552
Posted By GenoMax
You could take an example sequence and then use...

You could take an example sequence and then use "bbduk.sh" from BBMap suite in filter mode to extract reads containing that sequence with "literal=sequence_you_want" option. Guide to use bbduk is...
Forum: Bioinformatics 06-12-2019, 07:13 AM
Replies: 28
Views: 10,149
Posted By GenoMax
@jylee:...

@jylee: "/global/projectb/sandbox/gaag/bbtools/hg19/ref/genome/1/summary.txt" appears to refer to a location on JGI servers (if that is not your own). You will need to download and provide hg19...
Forum: Bioinformatics 06-12-2019, 07:05 AM
Replies: 235
Views: 77,589
Posted By GenoMax
@bwbubb: Option for reformat.sh that you are...

@bwbubb: Option for reformat.sh that you are looking for is "pairedonly=f Toss reads that are not mapped as proper pairs". Set pairedonly=t and process your BAM files.
Forum: Bioinformatics 06-10-2019, 07:53 AM
Replies: 19
Views: 2,959
Posted By GenoMax
@sahil: Please go through this UNIX basics...

@sahil: Please go through this UNIX basics tutorial (http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1), if you are unfamiliar with the command line.
Forum: Pacific Biosciences 06-06-2019, 04:08 AM
Replies: 3
Views: 507
Posted By GenoMax
If you are planning to use SMRTlink then use the...

If you are planning to use SMRTlink then use the bax and bas files.

There are other options like flye (https://github.com/fenderglass/Flye ) and canu (https://github.com/marbl/canu) that may be...
Forum: Bioinformatics 06-06-2019, 03:27 AM
Replies: 3
Views: 438
Posted By GenoMax
You can use Entrezdirect ...

You can use Entrezdirect (http://bit.ly/entrez-direct)utilities to query Pubmed database.


$ esearch -db pubmed -query "BRCA2 [GENE]" | esummary -format docsum | xtract -pattern DocumentSummary...
Forum: Bioinformatics 06-05-2019, 08:03 AM
Replies: 1
Views: 290
Posted By GenoMax
I suggest that you email Brian Bushnell directly...

I suggest that you email Brian Bushnell directly about this. You can find his email address in the bbmap source.
Forum: Illumina/Solexa 05-26-2019, 04:01 AM
Replies: 11
Views: 852
Posted By GenoMax
@potomac: While it is tempting to have bragging...

@potomac: While it is tempting to have bragging rights of having the latest and greatest in house it is difficult to keep the beast fed (when reagents for an S4 run cost upwards of $30K). Need for...
Forum: Illumina/Solexa 05-24-2019, 10:16 AM
Replies: 11
Views: 852
Posted By GenoMax
That may be partly true but we have no real idea...

That may be partly true but we have no real idea of what the manufacturing costs for Illumina are for any of these reagents. Since they are the sole suppliers they get to set the price. They can make...
Forum: Bioinformatics 05-24-2019, 09:57 AM
Replies: 107
Views: 23,761
Posted By GenoMax
Illumina's software pre-processing takes care of...

Illumina's software pre-processing takes care of clusters that may be showing mixed signals etc so they may never pass that step. Spantiles=t is mainly for nextSeq, where the clusters are hugh...
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