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Forum: Bioinformatics 11-07-2017, 09:06 AM
Replies: 636
Views: 121,921
Posted By santiagorevale
So, I've spoken with 10X support. For now they...

So, I've spoken with 10X support. For now they are not doing or planning to do any filtering step on the rawdata. However, thanks to my email they've opened a software feature request. Running...
Forum: Bioinformatics 11-07-2017, 08:59 AM
Replies: 211
Views: 50,784
Posted By santiagorevale
I tried running it in a computer with 8Gb of RAM...

I tried running it in a computer with 8Gb of RAM and in cluster nodes using a -Xmx limit of 18Gb and 24Gb (the max memory of the nodes is between 96 and 128 Gb).

Before I wasn't saying that...
Forum: Bioinformatics 11-07-2017, 05:00 AM
Replies: 211
Views: 50,784
Posted By santiagorevale
Hi GenoMax, Because I'm running this in a...

Hi GenoMax,

Because I'm running this in a cluster, to get more memory means to get more cores (slots), and processes requiring more cores take longer to be executed. Also, I was running this...
Forum: Bioinformatics 11-06-2017, 03:31 AM
Replies: 636
Views: 121,921
Posted By santiagorevale
Yes, that's how I'm running mkfastq. The...

Yes, that's how I'm running mkfastq. The sequencing is currently producing 2x75 bp, but by running mkfastq with the above mention cycle pattern: Read 1 is being trimmed to 26 bp, and for Read 2, we...
Forum: Bioinformatics 11-03-2017, 09:02 AM
Replies: 636
Views: 121,921
Posted By santiagorevale
Oh, sorry if I was not clear enough. Those are...

Oh, sorry if I was not clear enough. Those are the sequencing cycles not how I'm doing the base calling.

I've been working on 10X projects for several months now and evaluating them in different...
Forum: Bioinformatics 11-03-2017, 08:35 AM
Replies: 636
Views: 121,921
Posted By santiagorevale
Regarding the issue that produces the Ns, it's...

Regarding the issue that produces the Ns, it's not supported by them, because it occurs when sequencing on a HiSeq 4000 using 75,8,0,75 bp cycle pattern instead of their recommended 26,8,98 bp...
Forum: Bioinformatics 11-03-2017, 08:21 AM
Replies: 636
Views: 121,921
Posted By santiagorevale
cellranger pipeline is splitted in two steps:...

cellranger pipeline is splitted in two steps: "cellranger mkfastq" which produces the three above mentioned files (R1, R2, I1) and "cellranger count" which uses this 3 files as input.

The reason...
Forum: Bioinformatics 11-03-2017, 08:04 AM
Replies: 636
Views: 121,921
Posted By santiagorevale
Hi Genomax, I'm using 10Xs cellranger...

Hi Genomax,

I'm using 10Xs cellranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).

In this particular configuration,...
Forum: Bioinformatics 11-03-2017, 07:38 AM
Replies: 636
Views: 121,921
Posted By santiagorevale
Hi Brian, Would it be possible to add to...

Hi Brian,

Would it be possible to add to bbduk the capability of filtering also the Illumina Index file? Just to clarify what I mean, Illumina produces the following 3 output files for a typical...
Forum: Bioinformatics 11-02-2017, 08:32 AM
Replies: 211
Views: 50,784
Posted By santiagorevale
Hi there, Any hint on what I've previously...

Hi there,

Any hint on what I've previously asked?

Thanks!
Forum: Bioinformatics 10-23-2017, 05:43 AM
Replies: 211
Views: 50,784
Posted By santiagorevale
Hi Brian, I'm using "filterbyname.sh" script...

Hi Brian,

I'm using "filterbyname.sh" script from bbmap v37.60 (using Java 1.8.0_102) to extract some reads from a FastQ file given a list of IDs.

The current FastQ file has 196 Mi reads and I...
Forum: Bioinformatics 10-20-2017, 03:56 AM
Replies: 16
Views: 4,218
Posted By santiagorevale
Sorry if the same post appears many times. I'm...

Sorry if the same post appears many times. I'm having issues with the browser and am not getting feedback after posting. If all the postings appears, just keep the last one. Thanks!
Forum: Bioinformatics 10-20-2017, 01:27 AM
Replies: 16
Views: 4,218
Posted By santiagorevale
Hi Brian, I have a couple of questions about...

Hi Brian,

I have a couple of questions about this script:

1) does it work by default for patterned flowcells, like the ones for a HiSeq 4000? Or do I need to run it with some specific options,...
Forum: Bioinformatics 12-21-2016, 04:55 AM
Replies: 83
Views: 12,973
Posted By santiagorevale
Hi Brian, Thanks for the clarification! I'll be...

Hi Brian, Thanks for the clarification! I'll be waiting for the new clumpify update then. Happy a happy holidays!
Forum: Bioinformatics 12-20-2016, 09:45 AM
Replies: 83
Views: 12,973
Posted By santiagorevale
Oh, thanks! The "threads" option is missing from...

Oh, thanks! The "threads" option is missing from the command documentation. Also, how should I tell the program to run using pigz/pbzip2 (instead of gzip/bzip2)? Does it automatically detect them or...
Forum: Bioinformatics 12-20-2016, 09:17 AM
Replies: 83
Views: 12,973
Posted By santiagorevale
Hi Brian, Thank you very much for both...

Hi Brian,

Thank you very much for both (quick) replies. I've another question: could you tell me the amount of cores needed to run clumpify? Because I work in a cluster environment (using SGE) and...
Forum: Bioinformatics 12-20-2016, 06:50 AM
Replies: 83
Views: 12,973
Posted By santiagorevale
Hi Brian, I was wondering if you have any...

Hi Brian,

I was wondering if you have any plans for developing the above mentioned change in a short while (and if yes, when?), because I'm eager to implement Clumpify on our rawdata but I don't...
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