SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.06 seconds.
Search: Posts Made By: GenoMax
Forum: RNA Sequencing 01-11-2019, 11:41 AM
Replies: 1
Views: 197
Posted By GenoMax
You should contact 10x genomics tech support with...

You should contact 10x genomics tech support with this question. Post the info here when you hear from them so others can reference it in future.
Forum: Vendor Forum 01-09-2019, 03:10 PM
Replies: 2
Views: 260
Posted By GenoMax
Just curious which PacBio machine you are using...

Just curious which PacBio machine you are using for this service? Sequel?
Forum: Bioinformatics 01-09-2019, 03:09 PM
Replies: 2
Views: 197
Posted By GenoMax
#1 = Unless there is/are SNP's which are captured...

#1 = Unless there is/are SNP's which are captured by that particular read you would not be able to tell where the read came from. I assume the sequence of the gene is otherwise identical?
Forum: Bioinformatics 01-09-2019, 03:07 PM
Replies: 1
Views: 146
Posted By GenoMax
Cross-posted and answered on Biostars:...

Cross-posted and answered on Biostars: https://www.biostars.org/p/357359/#357497
Forum: Bioinformatics 01-06-2019, 06:25 PM
Replies: 312
Views: 91,244
Posted By GenoMax
@Seb: Brian does not seem to have time to respond...

@Seb: Brian does not seem to have time to respond to questions in this forum now a days but the different length of the adapters may have some bearing on this. Since the part you are looking for is...
Forum: Bioinformatics 01-04-2019, 12:33 PM
Replies: 3
Views: 424
Posted By GenoMax
You could also post this on Biostars.org using...

You could also post this on Biostars.org using "News" category.
Forum: Bioinformatics 12-20-2018, 05:05 AM
Replies: 312
Views: 91,244
Posted By GenoMax
@enma_ai: It is a bad idea to have spaces in your...

@enma_ai: It is a bad idea to have spaces in your file/directory names (even though your OS may allow it). I suggest the you change "NGS 10273-Raw" to "NGS_10273-Raw" and see if that fixes the error...
Forum: Illumina/Solexa 12-20-2018, 05:02 AM
Replies: 7
Views: 651
Posted By GenoMax
MiSeq is a sequencing champ as far as illumina...

MiSeq is a sequencing champ as far as illumina libraries are concerned. We look at results from MiSeq nano runs only qualitatively (rather than quantitatively) before the pools are transferred for...
Forum: 454 Pyrosequencing 12-18-2018, 08:51 AM
Replies: 3
Views: 810
Posted By GenoMax
Looks like they did. No obvious...

Looks like they did. No obvious announcements/comments from pundits anywhere either (google does not seem to bring anything up other than Qiagen's own site). Must be an application specific release.
Forum: General 12-11-2018, 08:35 AM
Replies: 1
Views: 315
Posted By GenoMax
In US, FDA has approved the following tests. All...

In US, FDA has approved the following tests. All other uses are in research settings.

https://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm330711.htm...
Forum: Illumina/Solexa 12-10-2018, 04:01 AM
Replies: 8
Views: 1,356
Posted By GenoMax
I am glad things worked to your satisfaction....

I am glad things worked to your satisfaction. Thanks for providing a final update.
Forum: Bioinformatics 12-10-2018, 03:59 AM
Replies: 1
Views: 267
Posted By GenoMax
If samples are truly absent then you may not get...

If samples are truly absent then you may not get any reads assigned to them as long as your libraries are excellent quality and run has worked well.

That said if you allow errors during...
Forum: Bioinformatics 12-06-2018, 08:02 AM
Replies: 6
Views: 646
Posted By GenoMax
AFAIK, as long as you have enough memory...

AFAIK, as long as you have enough memory everything that works on a normal ubuntu machine should work on WSL as well (assuming you installed ubuntu).
Forum: Bioinformatics 12-06-2018, 04:55 AM
Replies: 3
Views: 293
Posted By GenoMax
You could also try to do this analysis in one...

You could also try to do this analysis in one step. Use bbsplit.sh from BBMap (http://seqanswers.com/forums/showthread.php?t=41288) with both genomes. Look for reads that map to both genomes. Those...
Forum: Bioinformatics 12-06-2018, 04:46 AM
Replies: 3
Views: 293
Posted By GenoMax
You can grab the header from your bam file by...

You can grab the header from your bam file by doing samtools view -H your.bam > header.txt That can then be added back to your filtered sam.
Forum: RNA Sequencing 12-03-2018, 03:56 PM
Replies: 1
Views: 467
Posted By GenoMax
At this point there is no reason to use TopHat...

At this point there is no reason to use TopHat for RNAseq analysis. There are current options like STAR, BBMap, HISAT2 which should be used.
Forum: Bioinformatics 11-30-2018, 06:57 AM
Replies: 1
Views: 389
Posted By GenoMax
You can use bbduk from BBMap suite...

You can use bbduk from BBMap suite (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) to remove adapter contamination. BBMap suite is pure java so it will work on windows...
Forum: Bioinformatics 11-30-2018, 06:54 AM
Replies: 1
Views: 493
Posted By GenoMax
I suggest that you use bbsplit.sh from BBMap...

I suggest that you use bbsplit.sh from BBMap suite (http://seqanswers.com/forums/showthread.php?t=41288) along with a copy of rDNA repeat (if available) for your organism to bin reads into rRNA and...
Forum: Illumina/Solexa 11-30-2018, 06:52 AM
Replies: 7
Views: 749
Posted By GenoMax
@misterc: Problem is a lot of times users (or...

@misterc: Problem is a lot of times users (or even the facility techs) may create samplesheets using IEM elsewhere and then bring those to the machine at the time of run-start. People may also want...
Forum: Illumina/Solexa 11-26-2018, 04:39 PM
Replies: 7
Views: 749
Posted By GenoMax
You should leave your MiSeq as is. Isolating...

You should leave your MiSeq as is. Isolating instrument computers from open internet with a strong firewall (preferably via a defined/separate VLAN) is the best option for securing instrument...
Forum: Bioinformatics 11-26-2018, 12:15 PM
Replies: 4
Views: 267
Posted By GenoMax
Use -r [<chr>:]<start>..<end> format in your...

Use -r [<chr>:]<start>..<end> format in your command.
Forum: Bioinformatics 11-26-2018, 12:05 PM
Replies: 4
Views: 267
Posted By GenoMax
You could potentially trim your gff file to...

You could potentially trim your gff file to contain just the chromosome you want.
Forum: Bioinformatics 11-26-2018, 08:00 AM
Replies: 2
Views: 301
Posted By GenoMax
Take a look at bbsplit...

Take a look at bbsplit (http://seqanswers.com/forums/showthread.php?t=41288) from BBMap suite.

There are other tools like XenofilteR ...
Forum: RNA Sequencing 11-04-2018, 04:57 PM
Replies: 1
Views: 614
Posted By GenoMax
If you are using a specific kit then follow the...

If you are using a specific kit then follow the directions included with the kit for processing of data.
Forum: Illumina/Solexa 11-02-2018, 04:27 AM
Replies: 8
Views: 1,356
Posted By GenoMax
MiSeq is the champ of sequencing difficult...

MiSeq is the champ of sequencing difficult libraries. I would not compare success on a MiSeq to a different sequencer for odd libraries. If you are running an un-supported application then you are on...
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 07:55 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO