SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.06 seconds.
Search: Posts Made By: GenoMax
Forum: 454 Pyrosequencing Today, 08:51 AM
Replies: 1
Views: 46
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: 121
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: 1,128
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: 160
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: 427
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: 247
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: 247
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: 331
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: 354
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: 450
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: 5
Views: 528
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: 5
Views: 528
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: 215
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: 215
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: 233
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: 483
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: 1,128
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...
Forum: Bioinformatics 10-29-2018, 04:57 AM
Replies: 658
Views: 140,708
Posted By GenoMax
@1989sn1027: Brian has not been participating on...

@1989sn1027: Brian has not been participating on SA for last few months. You could try to create a ticket (https://sourceforge.net/p/bbmap/tickets/)at Source Forge and see if he responds to this...
Forum: Bioinformatics 10-25-2018, 04:02 AM
Replies: 658
Views: 140,708
Posted By GenoMax
I see that you are assigning 60G of RAM. Have you...

I see that you are assigning 60G of RAM. Have you tried to assign more and see if it helps?
Forum: General 10-24-2018, 10:04 AM
Replies: 1
Views: 493
Posted By GenoMax
You could use bbsplit.sh from BBMap to figure...

You could use bbsplit.sh from BBMap to figure this out in one step. Take a look at this thread (http://seqanswers.com/forums/showthread.php?t=41288)about how to do this.

If you already have the...
Forum: RNA Sequencing 10-17-2018, 09:10 AM
Replies: 5
Views: 885
Posted By GenoMax
Not likely. For a sequencer it is just DNA. Does...

Not likely. For a sequencer it is just DNA. Does not matter if it came from rRNA or some other gene. If the two sets of runs happened on two different chemistries or different machines then may be...
Forum: Illumina/Solexa 10-12-2018, 07:24 AM
Replies: 2
Views: 707
Posted By GenoMax
This data must have been sequenced on NextSeq (or...

This data must have been sequenced on NextSeq (or NovaSeq). That string of "G" is probably no-signal which is interpreted as G base.

The bias at the beginning of the reads is likely due to the...
Forum: Illumina/Solexa 10-09-2018, 09:29 AM
Replies: 2
Views: 528
Posted By GenoMax
1. Yes (AFAIK). 2. Quality will be lower for...

1. Yes (AFAIK).
2. Quality will be lower for the last set of cycles. Depending on your library quality (and nucloetide diversity) that effect may be more or less pronounced.
3. Index reads are...
Forum: Bioinformatics 10-04-2018, 05:41 AM
Replies: 308
Views: 88,564
Posted By GenoMax
@FlySquirrelFly: It has become difficult to get a...

@FlySquirrelFly: It has become difficult to get a hold of Brian (due to his day job responsibilities) but I will flag your post for him to see if he can respond.

I recall from some past discussion...
Forum: Bioinformatics 09-27-2018, 06:31 PM
Replies: 2
Views: 435
Posted By GenoMax
Search EBI-ENA for minION. Here is a...

Search EBI-ENA for minION. Here is a representative search (https://www.ebi.ac.uk/ena/data/search?query=minion%2C+bacteria). Click on categories on the left (experiment is a good one).
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 11:38 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO