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Search: Posts Made By: dsobral
Forum: Vendor Forum 02-27-2017, 08:57 AM
Replies: 108
Views: 52,539
Posted By dsobral
Just to add our 2 cents. We have a MiSeq...

Just to add our 2 cents.

We have a MiSeq running since 2013, and after some hickups we're now stable with it and reasonably happy.

We just recently installed a NextSeq500 and our first tests...
Forum: Illumina/Solexa 12-12-2013, 08:46 AM
Replies: 19
Views: 13,035
Posted By dsobral
I'm inclined to think something like that...

I'm inclined to think something like that happened. I'll try to see with the sequencing folks...



The fraction that went to undetermined is roughly 5-10% (depending on mismatches in the index)....
Forum: Illumina/Solexa 12-12-2013, 08:29 AM
Replies: 19
Views: 13,035
Posted By dsobral
FYI, just a note on what I got so far: The...

FYI, just a note on what I got so far:
The indexes from the "missing" sample are "TAGGCATG" and "TAGATCGC" (TAGGCAT-TAGATCG in the sample sheet).

Looking at the most abundant indexes in the...
Forum: Illumina/Solexa 12-12-2013, 08:01 AM
Replies: 19
Views: 13,035
Posted By dsobral
Just run bcl2fastq with the full run and correct...

Just run bcl2fastq with the full run and correct samplesheet.

The results show the same pattern as before: there is one "missing" sample with (almost) no data (1500-2000 reads playing with the...
Forum: Illumina/Solexa 12-12-2013, 03:45 AM
Replies: 19
Views: 13,035
Posted By dsobral
Ok, I now really read the sample sheet definition...

Ok, I now really read the sample sheet definition that is on the bcl2fastq user guide. Since I already had a sample sheet I assumed it was that one... didn't realize at first that it was something so...
Forum: Illumina/Solexa 12-12-2013, 02:16 AM
Replies: 19
Views: 13,035
Posted By dsobral
Thanks for the help. Indeed I have a...

Thanks for the help.

Indeed I have a SampleSheet in the input directory, which looks exacty like the one GenoMax showed. But this format does not seem to work with bcl2fastq.

I could see that...
Forum: Illumina/Solexa 12-11-2013, 02:03 PM
Replies: 19
Views: 13,035
Posted By dsobral
They usually only provide the fastq, but given...

They usually only provide the fastq, but given this issue, I asked them the full folder, so I should have all the files.

Right now the problem I'm having when running is that it does not seem to...
Forum: Illumina/Solexa 12-11-2013, 02:02 PM
Replies: 19
Views: 13,035
Posted By dsobral
My reads were also generated using MSR and they...

My reads were also generated using MSR and they don't have that tag at the end. (would be really nice though!)
Forum: Bioinformatics 12-11-2013, 12:31 PM
Replies: 17
Views: 8,867
Posted By dsobral
Thanks. I'm continuing this in the other thread: ...

Thanks. I'm continuing this in the other thread:
http://seqanswers.com/forums/showthread.php?t=39153

Daniel
Forum: Illumina/Solexa 12-11-2013, 12:27 PM
Replies: 19
Views: 13,035
Posted By dsobral
I'm working with them to try to figure out what...

I'm working with them to try to figure out what might have gone wrong.



I don't know the exact numbers but I think they had a bit of a high value in a couple of runs. Overclustering affects...
Forum: Bioinformatics 12-11-2013, 12:13 PM
Replies: 17
Views: 8,867
Posted By dsobral
Yes, I'm reading the documentation from here: ...

Yes, I'm reading the documentation from here:
http://supportres.illumina.com/documents/documentation/software_documentation/bcl2fastq/bcl2fastq_letterbooklet_15038058brpmi.pdf

It actually...
Forum: Illumina/Solexa 12-11-2013, 11:52 AM
Replies: 19
Views: 13,035
Posted By dsobral
Miseq: how to access index base calls? bcl2fastq does not work

Hello,

I get data from the local sequencing facility, where they use nextera and duel indexing in a MiSeq machine.

I have some issues with multiplexed samples, where sometimes a lot of...
Forum: Bioinformatics 12-11-2013, 11:26 AM
Replies: 17
Views: 8,867
Posted By dsobral
Unfortunately it doesn't work... e.g. locs file...

Unfortunately it doesn't work...
e.g. locs file are now clocs file, Assumes certain filenames that are different, etc... I don't think it was done for use with MiSeq.

Anyone has any experience...
Forum: Bioinformatics 12-11-2013, 10:31 AM
Replies: 17
Views: 8,867
Posted By dsobral
I had the same issue, and it was because of the...

I had the same issue, and it was because of the boost library version.

go to the redist folder in the bcl2fastq distribution, and build boost 1.44 that comes in there. Then make sure that...
Forum: Illumina/Solexa 12-10-2013, 06:13 AM
Replies: 7
Views: 1,935
Posted By dsobral
PS: although the data has these peculiarities, I...

PS: although the data has these peculiarities, I used these for denovo assembly of a bacteria, and it gave good results...

I just noticed because when I tried Edena on the full data, it complained...
Forum: Illumina/Solexa 12-10-2013, 06:11 AM
Replies: 7
Views: 1,935
Posted By dsobral
I didn't run it myself, but it was using Nextera...

I didn't run it myself, but it was using Nextera V2 250x250
Adaptor trimming was on (I guess by default)

Thanks,
Daniel
Forum: Illumina/Solexa 12-10-2013, 05:54 AM
Replies: 7
Views: 1,935
Posted By dsobral
I would understand if there was some obvious...

I would understand if there was some obvious consistency.
What I observe is that for the same run, read1 OR read2 can be either 250 or 251bp (and sometimes 249bp!) with no apparently consistent...
Forum: Illumina/Solexa 12-10-2013, 05:33 AM
Replies: 7
Views: 1,935
Posted By dsobral
Thanks for the reply. Very useful information. ...

Thanks for the reply. Very useful information.

The only thing I'm still puzzled is why some reads have 250bp and others have 251bp.

Daniel
Forum: Illumina/Solexa 12-10-2013, 05:09 AM
Replies: 7
Views: 1,935
Posted By dsobral
MiSeq fastq output: 250-251 bp reads

Hello,

I'm getting reads from a MiSeq machine and noticing that many have 251bp instead of 250bp, and that the last base has a highly skewed base composition. From what I read of the manual, the...
Forum: Illumina/Solexa 12-10-2013, 03:58 AM
Replies: 9
Views: 8,744
Posted By dsobral
How's the adapter trimming in most recent versions of MSR?

Just wandering if the reported "rampant" behavior is under control now.

Thanks,
Daniel
Forum: Illumina/Solexa 12-09-2013, 08:27 AM
Replies: 1
Views: 1,250
Posted By dsobral
PhiX SNPs and base recalibration?

Hi,

I was thinking of using PhiX library sequences from a run of our MiSeq to build a base calling error model and recalibrate our read qualities for other samples. First I would like to know if...
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