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Forum: Sample Prep / Library Generation 04-23-2019, 06:38 PM
Replies: 0
Views: 525
Posted By Him26
How does Twist Fast Hyb & Wash Kit work?

Hi,

Just came across this page which claim to cut down hyb time to 15min.
Has any one have experience with this product?
Dose it work with other products?

I would like to know how this...
Forum: Bioinformatics 03-30-2016, 06:10 PM
Replies: 4
Views: 1,753
Posted By Him26
I've tried to increase the memory to 48G and...

I've tried to increase the memory to 48G and still get the same error...
is there another reason for this?
Forum: Bioinformatics 03-09-2016, 03:17 PM
Replies: 2
Views: 1,112
Posted By Him26
My dumb mistake

Hi Alex,

Thank you for your reply.
I was looking through the gtf file and found that gtf file I was using had different 'chr' naming.
Gtf file I was using for the 1st mapping and 2nd mapping...
Forum: Bioinformatics 02-29-2016, 01:04 AM
Replies: 2
Views: 1,112
Posted By Him26
STAR mapping error

Hi, I am using STAR to find fusion transcripts and may be use cufflinks to quantify the transcripts. below is my command for 2ndpass mapping.

$STAR_HOME/STAR --runThreadN $CORE \
...
Forum: RNA Sequencing 02-28-2016, 07:36 PM
Replies: 6
Views: 1,903
Posted By Him26
Nope

I got caught up with other issue and have not followed up on this matter. sorry about this. Do let me know if you find out anything.:confused:
Forum: Bioinformatics 02-26-2016, 03:32 AM
Replies: 4
Views: 1,753
Posted By Him26
qualimap rnaseq error

Hi I am trying to run qualimap rnaseq and I get the following error

Failed to run rnaseq
net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename...
Forum: Bioinformatics 02-26-2016, 01:31 AM
Replies: 1
Views: 1,449
Posted By Him26
RseQC geneBody_coverage.py error

Hi, I am trying to run geneBody_coverage.py and I get the following error.
I assume the BinnedBitSet has something to do with transcript legnth so I removed ones that are longer than 500Kb.
But...
Forum: RNA Sequencing 07-27-2015, 04:46 PM
Replies: 6
Views: 1,903
Posted By Him26
Thank you for the reply. Brian Bushnell :...

Thank you for the reply.

Brian Bushnell : Yes the READ1 and READ2 are being substituted with actual fastq file names.
Are there more strange things you could find in my commend? please let me...
Forum: RNA Sequencing 07-26-2015, 04:23 PM
Replies: 6
Views: 1,903
Posted By Him26
Is this segemehl error due to memory?

Hi I am fairly new to RNA-seq.
I am trying to analyze my data using segemehl but am running into following error. (I've cut and pasted the last part of the output.)
[SEGEMEHL] Fri Jul 24 19:16:53...
Forum: RNA Sequencing 06-23-2015, 04:54 PM
Replies: 2
Views: 2,566
Posted By Him26
Hi, I am interested in performing RNAseq on FFPE...

Hi, I am interested in performing RNAseq on FFPE samples. I see lots of papers on google but I was wondering if you would share your experience. Thank you.
Forum: Bioinformatics 11-20-2013, 02:57 PM
Replies: 8
Views: 8,990
Posted By Him26
I have a slightly unrelated question. It's about...

I have a slightly unrelated question. It's about the plot.
Why is the variance low for low mean ? shouldn't it start high and decrease as the mean increase?
I have a similar data set and even if...
Forum: Bioinformatics 11-09-2013, 04:32 AM
Replies: 18
Views: 24,292
Posted By Him26
Thumbs up Thank you dpryan for the quick reply. I tried...

Thank you dpryan for the quick reply.
I tried the following code and I get the following error? any suggestions?

samtools sort -on -m 300000000 accepted_hits.bam |samtools view -h -...
Forum: Bioinformatics 11-08-2013, 04:46 PM
Replies: 18
Views: 24,292
Posted By Him26
samtools sort -on - output | samtools view -h - |...

samtools sort -on - output | samtools view -h - | htseq_count etc.

Could you expand on how you pipe-in to htseq-count?
I get an error saying I need to provide two arguments to htseq-count.
I...
Forum: Bioinformatics 10-05-2012, 01:56 PM
Replies: 1
Views: 1,220
Posted By Him26
Cufflinks stuck at assembling transcript and initialing abundances step

Dear authors of cufflinks,

I have many samples that gives me headache. I have paired end RNAseq data that were generated by Illumina Hiseq 2000. I hard trim the reads at Q score of 30 (~75bp)....
Forum: Bioinformatics 06-30-2012, 10:34 PM
Replies: 30
Views: 17,236
Posted By Him26
response

Thank you Arthur,

I have five bio reps. I don't think the plot uses log scale.
I used the following to estimate the function.

estimateDispersions( cds,...
Forum: Bioinformatics 06-29-2012, 04:35 PM
Replies: 30
Views: 17,236
Posted By Him26
Dispersion plot

HI,

I am completely newbie in regards to statistics.
I've been following Seqanswers forum and published papers on how to go about analyzing the data.
I have a two normal vs. two drug treated...
Forum: Bioinformatics 04-20-2012, 10:50 AM
Replies: 1
Views: 1,929
Posted By Him26
The solution to the problem was to rebuild the...

The solution to the problem was to rebuild the database.

>library(cummerbund)
>cuff<-readCufflinks(rebuild=T)

After rebuilding it worked fine.
Thank you.
Forum: Bioinformatics 04-20-2012, 05:48 AM
Replies: 1
Views: 1,929
Posted By Him26
Question CummeRbund Volcanoplot error

HI,
I am a newbie and I started using cummeRbund about two weeks.
few days ago I upgraded the R version to 2.15 and cummerbund to 1.2.
ever since, when I try to plot volcanoplot I get a following...
Forum: RNA Sequencing 12-15-2011, 06:07 PM
Replies: 24
Views: 15,204
Posted By Him26
If you do correlations between amplified and...

If you do correlations between amplified and unamplified what would you get for R^2 values?
And how are you isolating single cells or ultra low RNAs?
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