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Forum: Bioinformatics 04-15-2016, 05:25 PM
Replies: 1
Views: 1,352
Posted By user 31888
illumina Interval List: 0- or 1-based?

Hi,

A bit confusing...
I am using a human reference genome (human_g1k_v37.fasta) from GATK, a Ensemble annotation file and the TruSeq Exome Targeted Regions Manifest v1.2...
Forum: Bioinformatics 04-13-2016, 02:46 PM
Replies: 0
Views: 1,281
Posted By user 31888
VCF file missing GT field - How to fix?

Hi,

I am using GATK DiagnoseTargets to get some stats about the coverage of my reads compared to an exome interval list.

For that, I am running the following command:
${java} -jar ${GATK} \
...
Forum: Bioinformatics 04-08-2016, 09:34 AM
Replies: 2
Views: 971
Posted By user 31888
You are right GenoMax ! The program needs to...

You are right GenoMax !

The program needs to look in the 'BaseCalls' directory.
Plus, the tree architecture needs to be conserved since it will call some files from 'InterOp' dir as well.
Forum: Bioinformatics 04-07-2016, 04:07 PM
Replies: 2
Views: 971
Posted By user 31888
Picard CheckIlluminaDirectory: BaseCalls file format not found

Hi,

I recently used the MiSeq for a 2 x 76 paired-end sequencing run.

I moved the 'L001' directory from BaseSpace to our cluster (with Picard 2.1.0; java 1.8.0_77)
The 'L001' directory...
Forum: Illumina/Solexa 03-31-2016, 07:06 PM
Replies: 2
Views: 1,133
Posted By user 31888
Truseq Exome Library Prep: amplification does not work

Hi,

I have 6 samples with which I am trying to make a library with Illumina TruSeq Exome Library Prep Kit (starting material was 100-300 ng).

The problem is that before the exome capture, the...
Forum: Illumina/Solexa 03-26-2016, 08:24 AM
Replies: 4
Views: 2,248
Posted By user 31888
Ok. I checked the concentration of the final...

Ok.
I checked the concentration of the final library with PicoGreen.

How do you QC the final pooled library?
Any method/kit in particular?
Forum: Illumina/Solexa 03-25-2016, 09:08 PM
Replies: 4
Views: 2,248
Posted By user 31888
MiSeq error: Through-focus peak did not exceed SNR threshold

Hi,

Using a 10 pM pooled library of 6 indexed samples (4 from FFPE + 2 from fresh tissues) prepared with TruSeq Exome kit, I got this error message when running on MiSeq with no data generated...
Forum: Bioinformatics 02-26-2016, 10:51 AM
Replies: 3
Views: 1,614
Posted By user 31888
Thanks GenoMax ! If Illumina's...

Thanks GenoMax !



If Illumina's software drops the last base, it should not be sequenced, right?
So, why requesting Picard to skip 1 base then?
I read several times that people apply 1 extra...
Forum: Bioinformatics 02-26-2016, 10:05 AM
Replies: 3
Views: 1,614
Posted By user 31888
Picard IlluminaBasecallsToSam: Read Structure

Hi,

I am trying to convert MiSeq .bcl files into uSAM with Picard tools 'CheckIlluminaDirectory', 'ExtractIlluminaBarcodes' and 'IlluminaBasecallsToSam'.

These commands require to provide the...
Forum: Sample Prep / Library Generation 01-31-2016, 07:19 PM
Replies: 7
Views: 2,362
Posted By user 31888
Thanks Luc and adam.geber for your replies ! ...

Thanks Luc and adam.geber for your replies !

So your point is that everything is potentially sequenceable if I plan to incorporate a fragmentation step in the library prep, assuming that the...
Forum: Sample Prep / Library Generation 01-30-2016, 01:52 PM
Replies: 7
Views: 2,362
Posted By user 31888
By "crude extracts" I mean the DNA and RNA...

By "crude extracts" I mean the DNA and RNA material I obtain after cell lysis, separation and purification using a commercial kit (QIAGEN for instance).

The tissues the DNA and RNA come from can...
Forum: Sample Prep / Library Generation 01-29-2016, 05:39 PM
Replies: 7
Views: 2,362
Posted By user 31888
crude DNA extract suitable for sequencing?

I would like to check the integrity of crude DNA and RNA samples extracted from tissues in order to know if it is worth keep going with library prep and sequencing (MiSeq or HiSeq).

(1) Is running...
Forum: Bioinformatics 01-29-2016, 05:13 PM
Replies: 7
Views: 2,859
Posted By user 31888
maybe see: ...

maybe see:
https://support.bioconductor.org/p/74677/#75002

But I ended up doing a fresh install of pretty much everything (R, Python, Bioconductor and associated packages), and it worked.
Forum: Bioinformatics 12-24-2015, 09:50 AM
Replies: 0
Views: 938
Posted By user 31888
Tutorial or documentation for using UCSC MySQL

see: https://www.biostars.org/p/170573/
Forum: Bioinformatics 11-17-2015, 12:33 PM
Replies: 7
Views: 2,859
Posted By user 31888
Stupid thought: could it be something like EOF or...

Stupid thought: could it be something like EOF or other formatting issue that differs between my sample.bam files and TxDb.Hsapiens.UCSC.hg19.knownGene?

(I am using a Linux cluster)
Forum: Bioinformatics 11-17-2015, 12:28 PM
Replies: 7
Views: 2,859
Posted By user 31888
My mistake, sorry. It is actually...

My mistake, sorry.

It is actually 'sample_2.bam.bai' (I edited my previous post)
Forum: Bioinformatics 11-17-2015, 12:12 PM
Replies: 7
Views: 2,859
Posted By user 31888
Thanks ginger for your reply ! Here are the...

Thanks ginger for your reply !

Here are the outputs:
> str(exByGn)
Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots
..@ unlistData :Formal class 'GRanges' [package...
Forum: Bioinformatics 11-17-2015, 08:20 AM
Replies: 92
Views: 36,114
Posted By user 31888
Any chance someone already encountered this kind...

Any chance someone already encountered this kind of summarizeOverlaps error?
http://seqanswers.com/forums/showthread.php?p=184806#post184806
Forum: Bioinformatics 11-16-2015, 03:18 PM
Replies: 7
Views: 2,859
Posted By user 31888
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error

I am trying to use the GAGE pathway analysis tutorial (https://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf) with 3 samples of paired-end RNA-Seq reads (placed...
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