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Search: Posts Made By: GenoMax
Forum: Bioinformatics Today, 06:32 AM
Replies: 228
Views: 75,629
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: 227
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: 245
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: 245
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: 245
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: 420
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: 228
Views: 75,629
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: 420
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: 9,750
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: 228
Views: 75,629
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: 2,768
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: 342
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: 349
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: 188
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: 699
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: 699
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: 23,360
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...
Forum: Bioinformatics 05-22-2019, 03:26 AM
Replies: 2
Views: 275
Posted By GenoMax
You will need to use the name of the database you...

You will need to use the name of the database you are looking to get information on.

$ blastdbcmd -db /path_to/blastv5/nt_v5 -info
Database: Nucleotide collection (nt)
51,045,413...
Forum: Bioinformatics 05-17-2019, 04:03 AM
Replies: 228
Views: 75,629
Posted By GenoMax
I think you are looking for the following options...

I think you are looking for the following options that are accessible from "reformat.sh".


Sam and bam processing options:

mappedonly=f Toss unmapped reads.
unmappedonly=f ...
Forum: Bioinformatics 05-10-2019, 03:24 AM
Replies: 1
Views: 350
Posted By GenoMax
You should consider using featureCounts...

You should consider using featureCounts (http://bioinf.wehi.edu.au/featureCounts/). You may not need a loop. You can feed all SAM files to featureCounts and generate a read count matrix directly.
...
Forum: Bioinformatics 05-09-2019, 04:46 AM
Replies: 4
Views: 384
Posted By GenoMax
I assume you have checked GATK support forums?...

I assume you have checked GATK support forums? You must not be the first person to have run into this? You may want to post there to get an official response. If you do please post the relevant link...
Forum: Illumina/Solexa 05-09-2019, 02:56 AM
Replies: 2
Views: 422
Posted By GenoMax
As long as you have a unique set of index...

As long as you have a unique set of index sequences it is certainly possible. The total yield from a FC is not going to change so that final read number will get divided into the samples you put in...
Forum: RNA Sequencing 05-08-2019, 03:17 AM
Replies: 2
Views: 450
Posted By GenoMax
What do you mean by "data consistency check"? ...

What do you mean by "data consistency check"?

RNASeQC (https://software.broadinstitute.org/cancer/cga/rna-seqc) is a general program for RNAseq QC.
Forum: Introductions 05-06-2019, 03:55 AM
Replies: 1
Views: 256
Posted By GenoMax
For general question related to biology you may...

For general question related to biology you may want to post on Biology stackexchange (https://biology.stackexchange.com/). This forum is mainly focused on next generation sequencing. If your...
Forum: Events / Conferences 05-02-2019, 11:04 AM
Replies: 0
Views: 317
Posted By GenoMax
ISMB bioinfo-core workshop call for lightning talks

Posting on behalf of bioinfo-core group:

We are organizing a workshop for members of bioinformatics core facilities (http://bioinfo-core.org) at ISMB/ECCB 2019 (https://www.iscb.org/ismbeccb2019)...
Showing results 1 to 25 of 500

 


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