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Search: Posts Made By: GenoMax
Forum: Bioinformatics 09-09-2018, 07:30 AM
Replies: 1
Views: 210
Posted By GenoMax
I would suggest that you use the Illumina...

I would suggest that you use the Illumina provided adapter sequence. BBMerge detection feature is good when you don't have that information a priori. There may be some sequencing errors in your reads...
Forum: Illumina/Solexa 09-02-2018, 04:53 AM
Replies: 1
Views: 214
Posted By GenoMax
You just have to live with the quality of the...

You just have to live with the quality of the reads you get. Illumina requires 25 cycles in first read to accurately calibrate Q scores. Your type of sequencing is common with "Drop-seq" like methods...
Forum: Illumina/Solexa 08-21-2018, 11:24 AM
Replies: 5
Views: 552
Posted By GenoMax
If you are referring to sequences in...

If you are referring to sequences in "undetermined" files then these reads contain indexes that don't fit expected results (based on the samplesheet that you provide that has SampleID_Index mapping)....
Forum: Bioinformatics 08-14-2018, 03:21 AM
Replies: 3
Views: 633
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: 633
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: 1,261
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: 7,442
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: 7,442
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: 1,387
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: 588
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: 1,086
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: 732
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: 1,086
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: 1,086
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: 15,475
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: 732
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: 15,036
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: 15,036
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: 15,036
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: 331
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: 349
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: 81,655
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: 132,193
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: 460
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: 81,655
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...
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