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Search: Posts Made By: dsidote
Forum: Bioinformatics 11-10-2011, 10:32 AM
Replies: 2
Views: 1,344
Posted By dsidote
Aside from the read counts, I would also like to...

Aside from the read counts, I would also like to know what bases this particular enzyme adds to the end of the miRNA during amplification. I tried using the local setting and it does change the way...
Forum: Bioinformatics 11-10-2011, 08:18 AM
Replies: 2
Views: 1,344
Posted By dsidote
SHRiMP alignment results for colorspace miRNA

I'm trying to use SHRiMP to analyze a miRNA dataset using AB colorspace reads. I noticed when looking at the alignments using the pretty print option (-P) that SHRiMP aligns bases to the end of a...
Forum: Academic/Non-Profit Jobs 07-27-2011, 07:34 AM
Replies: 0
Views: 1,830
Posted By dsidote
Director of Genomics Core, Waksman Institute

The Waksman Institute, located on the Rutgers University Piscataway campus, is currently looking for a Director of its Genomics Core Facility. Information about the facility can be found at...
Forum: RNA Sequencing 03-17-2011, 10:31 AM
Replies: 39
Views: 16,200
Posted By dsidote
We are a core facility and we use the ScriptSeq...

We are a core facility and we use the ScriptSeq kits for all of our Illumina RNA-Seq libraries. The results are just as good, if not better because of the strand information, than the Illumina kits.
Forum: SOLiD 03-03-2011, 12:10 PM
Replies: 8
Views: 2,159
Posted By dsidote
The F5 is only mapping about 40%. According to...

The F5 is only mapping about 40%. According to AB, 40-50% is the best they have observed for the F5 read.
Forum: SOLiD 03-03-2011, 10:42 AM
Replies: 8
Views: 2,159
Posted By dsidote
We were told the same thing when we collected...

We were told the same thing when we collected poor F5 paired-end data. We were sent new strip tubes for the F5 tag and a new lot of cleave 2.1 but the problem persists.
Forum: SOLiD 02-02-2011, 01:04 PM
Replies: 8
Views: 3,364
Posted By dsidote
We have been having barcode issues since moving...

We have been having barcode issues since moving to SOLiD4. We have found BC contamination in our samples, this was verified for us by AB. We used the higher number BCs (17-96) and found contamination...
Forum: Bioinformatics 01-18-2011, 01:59 PM
Replies: 0
Views: 1,084
Posted By dsidote
Bioscope clip vs mismatch

Does anyone know how bioscope decides to Hard Clip vs calling a mismatch ?

For eg :

1781_585_1567 0 validated 586867 54 34M1H * 0
0 ==================================...
Forum: SOLiD 01-12-2011, 03:03 AM
Replies: 3
Views: 2,485
Posted By dsidote
We were told its related to the cleave 2.1...

We were told its related to the cleave 2.1 reagent. AB thinks this reagent with lot #'s 1010014 and 1010016 is the cause.

Dave
Forum: Bioinformatics 11-25-2010, 07:33 AM
Replies: 1
Views: 2,312
Posted By dsidote
From within the mdust directory, open fastafile.c...

From within the mdust directory, open fastafile.c with vi or nano and delete the line '#include <malloc.h>'. It should be line 3. Save the file and then try 'make' again.
Forum: Illumina/Solexa 11-22-2010, 11:16 AM
Replies: 9
Views: 4,932
Posted By dsidote
I realize the OP asked about the HiSeq. We don't...

I realize the OP asked about the HiSeq. We don't have a HiSeq, but I wouldn't expect the results to be very different from the GAIIx since they use the same chemistry so I'll throw this out there for...
Forum: Bioinformatics 11-03-2010, 06:14 AM
Replies: 25
Views: 8,240
Posted By dsidote
Bacdirector, What did you use to trim your...

Bacdirector,

What did you use to trim your SOLiD reads?

Dave
Forum: Bioinformatics 10-08-2010, 06:12 AM
Replies: 35
Views: 11,476
Posted By dsidote
I used the precompiled version and it worked. Our...

I used the precompiled version and it worked. Our sysadmin is recompiling the code with dcjones patch, so as soon as that is done I will test it with unmodified data.

DerSeb: Did you try removing...
Forum: Bioinformatics 10-07-2010, 01:11 PM
Replies: 35
Views: 11,476
Posted By dsidote
Thanks dcjones. Much easier than messing with...

Thanks dcjones. Much easier than messing with multi-GB files.
Forum: Bioinformatics 10-07-2010, 10:25 AM
Replies: 35
Views: 11,476
Posted By dsidote
I emailed Daehwan and he said the command is ...

I emailed Daehwan and he said the command is

tophat --color --quals bowtie_color_index 1.csfasta 1.qual

You don't have to convert to fastq, but you do have to remove the header lines from the...
Forum: Bioinformatics 10-07-2010, 07:58 AM
Replies: 35
Views: 11,476
Posted By dsidote
Since I have many more reads then I need I just...

Since I have many more reads then I need I just removed all of the reads with missed colorcalls from the csfasta and qual files. It was about 1% of the total number of reads that got removed.
Forum: Bioinformatics 10-07-2010, 07:06 AM
Replies: 35
Views: 11,476
Posted By dsidote
I am running into the same problem. I converted...

I am running into the same problem. I converted from csfasta and qual to fastq using solid2fastq from the Bfast package.

The prep_reads.log says

prep_reads v1.1.0 (1604)...
Forum: SOLiD 10-05-2010, 01:38 PM
Replies: 11
Views: 3,859
Posted By dsidote
We have one too and our experiences are the same...

We have one too and our experiences are the same as FLeader. We have run 6 samples so far and all have been excellent.
Forum: Bioinformatics 09-29-2010, 08:43 AM
Replies: 1
Views: 1,723
Posted By dsidote
ScaleMP

We are considering whether ScapeMP's vSMP is comparable to a single box with 24 cores and 512GB of RAM. Does anyone have any first hand experience with ScaleMP?

Thanks.
Forum: Illumina/Solexa 08-12-2010, 07:28 AM
Replies: 2
Views: 3,677
Posted By dsidote
cbot cluster generation

HI,

Since receiving our cbot we have observed this pattern of uneven cluster density. We are using 8pM input. Has anyone else observed this pattern and/or know what's causing this?

Dave
Forum: Academic/Non-Profit Jobs 01-13-2010, 07:10 AM
Replies: 0
Views: 1,838
Posted By dsidote
Bioinformatician - Waksman Institute

Bioinformatician Research Assistant Professor

The Waksman Institute of Microbiology located on the New Brunswick campus of Rutgers University is seeking a highly motivated and talented...
Forum: Bioinformatics 12-03-2009, 06:09 PM
Replies: 18
Views: 10,259
Posted By dsidote
I'm not sure I understand what your asking. Are...

I'm not sure I understand what your asking. Are you referring to splice variants? If so, we wrote a perl script reads the file line by line and counted exons for each transcript. I can send it to you...
Forum: Bioinformatics 12-03-2009, 11:58 AM
Replies: 18
Views: 10,259
Posted By dsidote
We were able to get what we needed. Thanks!

We were able to get what we needed. Thanks!
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