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Search: Posts Made By: GenoMax
Forum: Bioinformatics Yesterday, 01:53 PM
Replies: 7
Views: 168
Posted By GenoMax
Use the code I have in this post...

Use the code I have in this post (https://www.biostars.org/p/270737/#270753) to enumerate all the different barcodes present in your file. That should give you an idea of the complexity of the...
Forum: Bioinformatics Yesterday, 12:53 PM
Replies: 7
Views: 168
Posted By GenoMax
I see. I have not personally used this feature...

I see. I have not personally used this feature since most of barcode work is done at the bcl2fastq stage, where you can allow for errors in sequence.

What exactly are you trying to do? Eliminate...
Forum: Bioinformatics Yesterday, 10:51 AM
Replies: 11
Views: 1,603
Posted By GenoMax
Not only Java but also Java development kit...

Not only Java but also Java development kit (JDK). From here (http://www.oracle.com/technetwork/java/javase/downloads/jdk9-downloads-3848520.html).
Forum: Bioinformatics Yesterday, 08:13 AM
Replies: 11
Views: 1,603
Posted By GenoMax
I assume you have the Java Development Kit...

I assume you have the Java Development Kit installed in addition to the JRE. If not, install JDK and then the DMG version of fastqc should work.
Forum: Bioinformatics Yesterday, 08:02 AM
Replies: 11
Views: 1,603
Posted By GenoMax
What do you mean by that? You can't open a fastq...

What do you mean by that? You can't open a fastq file or the program itself?
Forum: Bioinformatics Yesterday, 07:08 AM
Replies: 11
Views: 1,603
Posted By GenoMax
Are you downloading the macOS .dmg version here...

Are you downloading the macOS .dmg version here (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.dmg)?
Forum: Illumina/Solexa Yesterday, 06:51 AM
Replies: 2
Views: 79
Posted By GenoMax
Looks like you can mount that as a file share...

Looks like you can mount that as a file share (http://docs.aws.amazon.com/storagegateway/latest/userguide/getting-started-use-fileshare.html). So as long as it reliably stays connected you should be...
Forum: Bioinformatics Yesterday, 04:26 AM
Replies: 7
Views: 168
Posted By GenoMax
What barcode filter are you referring? Generally...

What barcode filter are you referring? Generally with "hdist=N" paramter you can allow or disallow (hdist=0) mismatches.
Forum: Illumina/Solexa 11-16-2017, 07:42 AM
Replies: 2
Views: 126
Posted By GenoMax
What are the expected insert sizes in both cases?...

What are the expected insert sizes in both cases? Keep in mind that in general short insert libraries will preferentially cluster (you may need to adjust loading conc going in, taking that into...
Forum: Bioinformatics 11-14-2017, 04:48 AM
Replies: 55
Views: 11,816
Posted By GenoMax
@Kate: You should take a look at tadpole.sh from...

@Kate: You should take a look at tadpole.sh from BBMap suite, which is a k-mer based aligner. Someone recently used it to assemble the axolotl genome so whatever you are working with may be feasible...
Forum: Bioinformatics 11-10-2017, 08:13 AM
Replies: 5
Views: 461
Posted By GenoMax
You can get the human rDNA repeat from here...

You can get the human rDNA repeat from here (https://www.ncbi.nlm.nih.gov/nuccore/U13369.1?report=fasta). If you do see contamination you can use bbsplit.sh from BBMap suite to separate those reads...
Forum: Bioinformatics 11-10-2017, 07:14 AM
Replies: 5
Views: 461
Posted By GenoMax
What organism are you working with?

What organism are you working with?
Forum: Bioinformatics 11-09-2017, 10:10 AM
Replies: 5
Views: 461
Posted By GenoMax
You should scan/trim your sequences with a...

You should scan/trim your sequences with a suitable program (bbduk.sh from BBMap, trimmomatic, cutadapt etc.). While some rely on aligners to soft-clip adapter sequences (and they likely will),...
Forum: Bioinformatics 11-07-2017, 07:27 AM
Replies: 187
Views: 38,531
Posted By GenoMax
While that is an odd restriction it is what it is...

While that is an odd restriction it is what it is when one is using shared compute resources.

Just for kicks have you tried to run this on a local desktop that has a decent amount of RAM (16G)?...
Forum: Illumina/Solexa 11-07-2017, 05:44 AM
Replies: 13
Views: 717
Posted By GenoMax
Don't be surprised. Keep in mind that small...

Don't be surprised. Keep in mind that small inserts preferentially cluster so if they are in there they are attaching to flowcell first.
Forum: Illumina/Solexa 11-07-2017, 05:05 AM
Replies: 13
Views: 717
Posted By GenoMax
@ATGCT: You should take this data and use BBMap...

@ATGCT: You should take this data and use BBMap to estimate the insert size. You can do it in different ways. See this link (http://seqanswers.com/forums/showpost.php?p=201970&postcount=2)for...
Forum: Bioinformatics 11-07-2017, 05:01 AM
Replies: 187
Views: 38,531
Posted By GenoMax
Perhaps. But if you have more memory why not...

Perhaps. But if you have more memory why not allocate more and see if that helps. Unless you are being charged by every megabyte you use ;)
Forum: Bioinformatics 11-07-2017, 04:57 AM
Replies: 1
Views: 284
Posted By GenoMax
Biologists you work with may already know these...

Biologists you work with may already know these but just in case. See if paper1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333867/), paper2...
Forum: Bioinformatics 11-06-2017, 11:47 AM
Replies: 3
Views: 280
Posted By GenoMax
Not answering your question directly but you...

Not answering your question directly but you could use "reformat.sh" from BBMap suite (https://sourceforge.net/projects/bbmap/) to do this as well. You can specify sampling parameters with more...
Forum: Bioinformatics 11-06-2017, 09:36 AM
Replies: 3
Views: 365
Posted By GenoMax
Using your example ...

Using your example (http://amigo.geneontology.org/amigo/search/bioentity?q=virus%20receptor)you can see that you are able to custom download the genes (blue button at the top right of the page). Add...
Forum: Bioinformatics 11-06-2017, 03:56 AM
Replies: 2
Views: 276
Posted By GenoMax
I think you are better off asking this question...

I think you are better off asking this question to JGI tech support who gave you this data.

@Brian Bushnell (author of BBMap) works at JGI and contributes regularly on this forum. He has been...
Forum: Bioinformatics 11-03-2017, 10:08 AM
Replies: 586
Views: 102,943
Posted By GenoMax
So how are you doing the base calling then? ...

So how are you doing the base calling then?

10x recommends that you run 26x8x98 but you are running this as a 75x8x75 run instead? If that is the case my recommendation above would cut the read 1...
Forum: Bioinformatics 11-03-2017, 09:51 AM
Replies: 586
Views: 102,943
Posted By GenoMax
Yikes! You are certainly doing something...

Yikes! You are certainly doing something completely off-label here :-)

In the cellranger mkfastq run, you could use a base-mask such as --use-bases-mask=Y26n*,I8,Y*. That should produce reads in...
Forum: Bioinformatics 11-03-2017, 09:26 AM
Replies: 586
Views: 102,943
Posted By GenoMax
While I have not worked with cellranger (I have...

While I have not worked with cellranger (I have only used longranger for WGS data) this sounds like an odd behavior. 10x should be accounting for presence of N's in the reads in their software.

If...
Forum: Bioinformatics 11-03-2017, 09:13 AM
Replies: 586
Views: 102,943
Posted By GenoMax
If you are using the cellranger pipeline then you...

If you are using the cellranger pipeline then you should not need to do anything to the data outside the pipeline. Cellranger pipeline takes in raw Illumina flowcell data folder and does the entire...
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