SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.07 seconds.
Search: Posts Made By: GenoMax
Forum: Bioinformatics 08-14-2018, 03:21 AM
Replies: 3
Views: 430
Posted By GenoMax
You can try running the job again while nothing...

You can try running the job again while nothing else is running on the machine. You may be able to just get away with it.
Forum: Bioinformatics 08-13-2018, 11:02 AM
Replies: 3
Views: 430
Posted By GenoMax
Does 4TB refer to disk space? bwa is looking for...

Does 4TB refer to disk space? bwa is looking for more RAM so my guess is you don't have 53G of free RAM available or you are not the only user on this server.
Forum: Pacific Biosciences 08-12-2018, 03:29 PM
Replies: 4
Views: 485
Posted By GenoMax
Appears to some kind of file permission issue....

Appears to some kind of file permission issue. You should report this to PacBio tech support directly.
Forum: Bioinformatics 08-12-2018, 03:27 PM
Replies: 26
Views: 6,949
Posted By GenoMax
"bbsplit.sh" is a general purpose tool that will...

"bbsplit.sh" is a general purpose tool that will bin reads into any number of bins (depending on the reference sequences provided, you can provide as many as you want). In this case you would provide...
Forum: Bioinformatics 08-12-2018, 05:01 AM
Replies: 26
Views: 6,949
Posted By GenoMax
Have you tried using "bbsplit.sh" with human...

Have you tried using "bbsplit.sh" with human genome to see if that works better. If you are interested in non-human data then I would use the non-masked genome and risk losing a few additional reads.
Forum: Introductions 08-10-2018, 09:39 AM
Replies: 3
Views: 1,127
Posted By GenoMax
@Gabriela: Take a look at http://allseq.com/ and...

@Gabriela: Take a look at http://allseq.com/ and https://genohub.com/ to do comparison shopping for sequencing prices.

You should always have at least 3 (or more if possible) biological replicates...
Forum: Bioinformatics 08-10-2018, 04:00 AM
Replies: 4
Views: 420
Posted By GenoMax
@landrjos: What you are describing is called an...

@landrjos: What you are describing is called an interleaved fastq file where R1 and R2 reads are present in a single file.

You can use reformat.sh from BBMap suite...
Forum: Illumina/Solexa 08-07-2018, 06:19 AM
Replies: 11
Views: 862
Posted By GenoMax
Glad to hear they are doing the right thing and...

Glad to hear they are doing the right thing and will re-sequence. Only thing you are out of is time.
Forum: Bioinformatics 08-03-2018, 05:16 AM
Replies: 5
Views: 627
Posted By GenoMax
Your indexes most likely look like Index1+Index2...

Your indexes most likely look like Index1+Index2 (e.g. GGACTCCT+GCGATCTA) then that is how you need to include them in the file one per line. Is that how you are doing this?
Forum: Illumina/Solexa 08-02-2018, 07:14 AM
Replies: 11
Views: 862
Posted By GenoMax
As you appropriately said above: That...

As you appropriately said above:



That needs to take priority.
Forum: Illumina/Solexa 08-02-2018, 07:01 AM
Replies: 11
Views: 862
Posted By GenoMax
You can use "filterbytile.sh" from BBMap suite...

You can use "filterbytile.sh" from BBMap suite (https://sourceforge.net/projects/bbmap/).

Has the sequence provider said anything about the possibility that there was a hardware/software problem...
Forum: Bioinformatics 08-02-2018, 05:08 AM
Replies: 25
Views: 15,065
Posted By GenoMax
You can use reformat.sh in=your_file.fastq...

You can use reformat.sh in=your_file.fastq out=newfile.fa to convert the reads to fasta format.

That said I think mapPacBio.sh should automatically split reads longer than 6k when it does...
Forum: Bioinformatics 07-31-2018, 03:29 AM
Replies: 5
Views: 627
Posted By GenoMax
Before we get into specifics can you ask your...

Before we get into specifics can you ask your sequence provider to do this demultiplexing with Illumina's program called bcl2fastq (you can't do this since it requires access to the full data folder...
Forum: Bioinformatics 07-23-2018, 10:15 AM
Replies: 90
Views: 14,493
Posted By GenoMax
I am able to do something like for i in `ls...

I am able to do something like

for i in `ls -1 *_1*.fastq | sed 's/_1.fastq//'`; do clumpify.sh -Xmx10g in1=$i\_1.fastq in2=$i\_2.fastq out1=$i\_clu_1.fastq out2=$i\_clu_2.fastq; done and have...
Forum: Bioinformatics 07-21-2018, 05:31 AM
Replies: 90
Views: 14,493
Posted By GenoMax
Are you using the latest version of BBMap? Have...

Are you using the latest version of BBMap? Have you tried to run a test with actual file names instead of shell variables?
Forum: Bioinformatics 07-21-2018, 04:16 AM
Replies: 90
Views: 14,493
Posted By GenoMax
It looks like out1= and out2= variables are not...

It looks like out1= and out2= variables are not being correctly expanded. BBMap seems to think that your outputs are inputs (in1=./Preproccesing/ERR522065/ERR522065_1_optical.fastq.gz,...
Forum: Bioinformatics 07-19-2018, 11:02 AM
Replies: 2
Views: 256
Posted By GenoMax
Help page ...

Help page (https://software.broadinstitute.org/software/igv/interpreting_insert_size)that describes the meaning of those colors.
Forum: Bioinformatics 07-19-2018, 03:59 AM
Replies: 1
Views: 277
Posted By GenoMax
I am not seeing anything that is an obvious red...

I am not seeing anything that is an obvious red flag. Getting warning in FastQC analysis is common and those need to be taken into consideration using the context of your experiment.

You will...
Forum: Bioinformatics 07-19-2018, 03:57 AM
Replies: 304
Views: 79,947
Posted By GenoMax
@jsena33: You should take a look at UMI tools ...

@jsena33: You should take a look at UMI tools (https://github.com/CGATOxford/UMI-tools)for this type of application.
Forum: Bioinformatics 07-17-2018, 01:59 PM
Replies: 646
Views: 129,808
Posted By GenoMax
Is your bbmap installed correctly? Have you moved...

Is your bbmap installed correctly? Have you moved any files around? I am able to run "bbfakereads.sh" and generate fastq and fasta files without a problem.
Forum: Bioinformatics 07-17-2018, 05:50 AM
Replies: 1
Views: 420
Posted By GenoMax
Export a network share from the CentOS server....

Export a network share from the CentOS server. Mount it on NextSeq 550. You can then choose that share as the destination to write data to. If you don't want to do it that way you could manually copy...
Forum: Bioinformatics 07-12-2018, 08:59 PM
Replies: 304
Views: 79,947
Posted By GenoMax
Have you looked at the in-line help for...

Have you looked at the in-line help for "splitnextera.sh"? The adapters for Mate Pair libraries are in the "adapters.fa" file so you should be able to trim them as usual...
Forum: Bioinformatics 07-11-2018, 01:07 AM
Replies: 2
Views: 469
Posted By GenoMax
You may want to recreate the indexes on WSL and...

You may want to recreate the indexes on WSL and retry. Is the memory availabe comparable on WSL and linux?
Forum: Bioinformatics 07-10-2018, 03:05 AM
Replies: 1
Views: 282
Posted By GenoMax
This is hardly ever the case. Now-a-days...

This is hardly ever the case. Now-a-days technical part of sequencing has become almost perfect. If a lane had some problem (e.g. a bubble during sequencing) your sequencing provider should not...
Forum: Bioinformatics 07-09-2018, 02:26 AM
Replies: 126
Views: 45,603
Posted By GenoMax
I would think so. I don't have first hand...

I would think so. I don't have first hand experience with mate pair reads but I recall that you need to switch one of the reads around.
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 08:03 PM.


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