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Forum: Bioinformatics 10-21-2013, 08:43 PM
Replies: 6
Views: 2,280
Posted By arkal
TruSeq exome capture.... FYI we saw it in rna seq...

TruSeq exome capture.... FYI we saw it in rna seq data also!
Forum: Bioinformatics 04-04-2013, 11:27 PM
Replies: 6
Views: 2,280
Posted By arkal
bump:confused:

bump:confused:
Forum: Bioinformatics 04-03-2013, 03:56 AM
Replies: 6
Views: 2,280
Posted By arkal
Question so i tried this with a couple of my samples vs...

so i tried this with a couple of my samples vs human.... i'm getting only 3% not mapping. So there is either very little or no contamination in my sample. So then what can explain the bimodal gc...
Forum: Bioinformatics 04-03-2013, 01:08 AM
Replies: 6
Views: 2,280
Posted By arkal
i don't know why the image is not being shown in...

i don't know why the image is not being shown in the post... here's the link

http://www.freeimagehosting.net/79wl3
Forum: Bioinformatics 04-02-2013, 08:23 PM
Replies: 6
Views: 2,280
Posted By arkal
Contamination in my sample?

Hi all!

I just ran a 100bp PE human exome seq run in my lab and was looking at the fastqc results of my run. I am getting this weird pattern in the gc content distribution and was wondering is...
Forum: Bioinformatics 03-19-2013, 05:25 AM
Replies: 14
Views: 25,549
Posted By arkal
kudos to you, my friend! works like a charm!

kudos to you, my friend! works like a charm!
Forum: Bioinformatics 10-16-2012, 11:12 PM
Replies: 1
Views: 1,717
Posted By arkal
FASTQC help

I'm not a java programmer so I need some help doing something I hope there's someone here who can assist!

According to the fastqc documentation, for calculating duplication levels it considers...
Forum: RNA Sequencing 10-16-2012, 11:00 PM
Replies: 3
Views: 1,302
Posted By arkal
If I may request, could you run a picard estimate...

If I may request, could you run a picard estimate library complexity on your bam and let me know the result? Because I'm apprehensive about the accuracy of the fastqc duplication results! My sample...
Forum: Bioinformatics 10-15-2012, 09:10 PM
Replies: 8
Views: 6,517
Posted By arkal
Question A trivial question: When you say overestimated,...

A trivial question: When you say overestimated, do u mean the duplication in his sample is LESS THAN 13% or MORE THAN 13%.
Forum: Bioinformatics 10-15-2012, 06:34 AM
Replies: 8
Views: 6,517
Posted By arkal
Lightbulb I had the same query. What i personally feel is...

I had the same query. What i personally feel is that Picard is more accurate.

My reassoning is that fastqc is calling around 70% duplication looking at only the read 1 file and a similar amount...
Forum: Illumina/Solexa 10-15-2012, 04:44 AM
Replies: 3
Views: 2,250
Posted By arkal
What he means is that if you haven't provided a...

What he means is that if you haven't provided a samplesheet.csv (and if tehre wasn't one in your sequencing directory) then CASAVA will not register multiplexed lanes and all samples in a multiplexed...
Forum: Bioinformatics 10-15-2012, 04:34 AM
Replies: 4
Views: 1,267
Posted By arkal
It's as TiborNagy said. When you are sequencing,...

It's as TiborNagy said. When you are sequencing, instead of separating different samples in a lane by barcoding you just put them in in the same concentrations so as to get a list of differences seen...
Forum: Bioinformatics 10-15-2012, 03:29 AM
Replies: 8
Views: 5,440
Posted By arkal
In my experience (from what i've seen and what...

In my experience (from what i've seen and what i've read), you can expect to see 60-90% duplication when u run a fastqc on ur data! Don't really know how it correlates to the real picture...
Forum: Sample Prep / Library Generation 09-27-2012, 05:11 AM
Replies: 3
Views: 4,600
Posted By arkal
Bioanalyzer expired RNA Nano 6000 kit

Hey!

I'm need to run a preliminary QC on my RNA samples but I've got a problem... My RNA Nano 6000 kit expired in june 2010 (yes yes lmao :D ).

I wanted to know whether only reagents have an...
Forum: Bioinformatics 08-08-2012, 10:55 PM
Replies: 1
Views: 1,267
Posted By arkal
dbsnp rod file for hg19

Hey!

So i want to run GATK tools on y data which i've aligned to hg19 and i need the dbsnp rod file for hg19 (i believe it's dbsnp_132_hg19.rod right?) but i can't find it anywhere :mad:

the...
Forum: Bioinformatics 07-30-2012, 11:30 PM
Replies: 4
Views: 1,481
Posted By arkal
You got a point there! It's not 100% only exons...

You got a point there! It's not 100% only exons and there may be unannotated regions. I hadn't considered that.

And yeah i'm running tophat now. I ran a BWA of my reads onto the trscpt ref first...
Forum: Bioinformatics 07-30-2012, 08:04 PM
Replies: 5
Views: 5,115
Posted By arkal
No worries :) all the best!

No worries :) all the best!
Forum: Bioinformatics 07-30-2012, 07:58 PM
Replies: 4
Views: 1,481
Posted By arkal
HEy thanks for your reply! Did you map your RNA...

HEy thanks for your reply! Did you map your RNA Seq data to a trasncriptome reference or to the HG18/19 Human Genome reference?

I've mapped my data to the Ensembl Transcriptome reference so...
Forum: Bioinformatics 07-30-2012, 03:34 AM
Replies: 5
Views: 5,115
Posted By arkal
It seems to be the same sample in different...

It seems to be the same sample in different lanes/runs... so you can either merge the fastqs and align or align the 3 separately and merge the sams! I recommend the latter as it will take less time...
Forum: Bioinformatics 07-30-2012, 01:49 AM
Replies: 5
Views: 5,115
Posted By arkal
Smile Process files separately then use comparitive...

Process files separately then use comparitive studies on the sam/bam files! :)
Forum: Bioinformatics 07-30-2012, 01:38 AM
Replies: 4
Views: 1,481
Posted By arkal
Question Perplexed!

Ok so this isn't really a problem per-say but i was just curious as to what it really means....

I ran picsrd's insert size metrics on my PE RNA Seq data (mapped to the Ensembl Transcriptome model)...
Forum: Bioinformatics 07-17-2012, 11:30 PM
Replies: 1
Views: 832
Posted By arkal
try sed -i s/">"/">chr"/g...

try

sed -i s/">"/">chr"/g <filename>
Forum: Bioinformatics 07-03-2012, 08:26 PM
Replies: 3
Views: 1,327
Posted By arkal
You can extract reads from a given region from...

You can extract reads from a given region from your sam/bam file. about assembling it ... u should be assemble it into a gene but about getting two haplotypes i can't say because then you would need...
Forum: Bioinformatics 07-03-2012, 08:18 PM
Replies: 7
Views: 4,980
Posted By arkal
Smile Sorry there my mistake... when you said you...

Sorry there my mistake... when you said you aligned genomes i automatically thought in terms of fastq onto ref fast alignment stored in the form of bams.
So in my opinion, what you CAN do instead...
Forum: Bioinformatics 07-02-2012, 07:59 PM
Replies: 4
Views: 1,244
Posted By arkal
Hmmm... you can try what they did in that...

Hmmm... you can try what they did in that paper.... align with strict criteria i guess to get better results... i'm not sure about RNA seq aligning but as i said, when i aligned DNA reads from a non...
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