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Search: Posts Made By: GenoMax
Forum: Bioinformatics 12-06-2018, 08:02 AM
Replies: 5
Views: 277
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: 180
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: 180
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: 285
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: 319
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: 389
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: 477
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: 477
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: 191
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: 191
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: 202
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: 453
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: 6
Views: 1,000
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: 139,873
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: 139,873
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: 440
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: 855
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: 671
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: 506
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: 87,864
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: 414
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).
Forum: Bioinformatics 09-27-2018, 05:23 AM
Replies: 4
Views: 411
Posted By GenoMax
This may be easier to do by obtaining the index...

This may be easier to do by obtaining the index read as a separate fastq file. You will also get real Q-scores for bases in index read when you do that. Stand-alone bcl2fastq allows one to get data...
Forum: Bioinformatics 09-26-2018, 12:01 PM
Replies: 4
Views: 411
Posted By GenoMax
Are you sure about that? Generally in case of...

Are you sure about that? Generally in case of Illumina sequencing index sequences (which are not part of actual reads) are transferred to the fastq header as a part of demultiplexing process. That is...
Forum: Bioinformatics 09-26-2018, 04:07 AM
Replies: 1
Views: 205
Posted By GenoMax
I am not sure what the size of BAM file you are...

I am not sure what the size of BAM file you are trying to use is but you could try adding the option "--java-mem-size=16G" to your qualimap command (Adjust RAM amount as needed). and see if that...
Forum: Illumina/Solexa 09-24-2018, 07:00 AM
Replies: 7
Views: 762
Posted By GenoMax
While likely let us hope that is not the case...

While likely let us hope that is not the case because otherwise you would be losing a lot of data to adapters and would have short reads.

When you have had a chance to investigate let us know...
Showing results 1 to 25 of 500

 


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