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Forum: Bioinformatics 01-11-2016, 10:34 AM
Replies: 0
Views: 594
Posted By biofreak
CNV detection for single patient sample

Hi
I am very new to CNV detection analysis. I have single sample of a patient for which want to find CNVs. Most of the CNV detection software expect lot of samples for the models to work...
Forum: Bioinformatics 09-01-2015, 07:46 AM
Replies: 1
Views: 730
Posted By biofreak
How to validate RNAseq pipeline

Hi
I have created a pipeline to process RNAseq data and have used DEseq to conduct differential expression analysis. The question is, how do I know it is giving valid results? Are there any gold...
Forum: Bioinformatics 08-09-2013, 01:04 PM
Replies: 1
Views: 737
Posted By biofreak
Error in CountOverlaps

hi
I get the following error when I run:
countOverlaps(exonRangesListtx[[hif1Ind[r]]], align)

In .Seqinfo.mergexy(x, y) :
Each of the 2 combined objects has sequence levels not in the other:...
Forum: Bioinformatics 06-09-2012, 03:39 AM
Replies: 5
Views: 2,104
Posted By biofreak
Simon, thanks for replying. Yes. I actually...

Simon,
thanks for replying.
Yes. I actually I had asked you the similar question before and you pointed me to the development version of DEseq (then) which takes care of those high variance and...
Forum: Bioinformatics 06-08-2012, 12:26 PM
Replies: 5
Views: 2,104
Posted By biofreak
thank you for the prompt reply. I'll dig more...

thank you for the prompt reply. I'll dig more into raw data like you suggested.
But what bothers me is that there is no correlation with the previous data! At least in my case. All the analysis...
Forum: Bioinformatics 06-08-2012, 11:57 AM
Replies: 5
Views: 2,104
Posted By biofreak
Differnt results with old and new DESeq package for RNAseq

hi
I had done some RNAseq analysis using the older (1.5) version of DESeq and obtained differentially expressed genes. I re-run the analysis on the same data using version 1.8.2.
The results are...
Forum: Bioinformatics 04-17-2012, 07:24 AM
Replies: 3
Views: 1,325
Posted By biofreak
thanks. How do I obtain exon.bed for rat?

thanks. How do I obtain exon.bed for rat?
Forum: Bioinformatics 04-17-2012, 07:11 AM
Replies: 18
Views: 2,413
Posted By biofreak
I ran barsplitter as follows: cat...

I ran barsplitter as follows:
cat combined.fastq | fastx_barcode_splitter.pl --bcfile ../barcode1.txt --bol --mismatches 1 --prefix "lane1" --suffix ".fastq"

It creates separate fastq files but...
Forum: Bioinformatics 04-17-2012, 07:02 AM
Replies: 18
Views: 2,413
Posted By biofreak
well my barcodes are not illumina but are nugen....

well my barcodes are not illumina but are nugen. I ran casava normally with the added
use-bases-mask parameter. it did not complain and generated fastq files. When I ran tophat with these files, ...
Forum: Bioinformatics 04-17-2012, 06:45 AM
Replies: 18
Views: 2,413
Posted By biofreak
yes. It did work.. I then split the fastq files...

yes. It did work.. I then split the fastq files per barcode using fastx barcode splitter. However, it still did not solve my problem of less number of reads being aligned after running tophat. ...
Forum: Bioinformatics 04-13-2012, 10:15 AM
Replies: 4
Views: 1,204
Posted By biofreak
fastx_barcode_splitter

I used fastx_barcode_splitter.pl to demultiplex the barcodes to generate separate fastq files. However the files still retain the barcodes (at the beginning of each sequence in my case) . I want to...
Forum: Bioinformatics 04-12-2012, 10:13 AM
Replies: 3
Views: 1,325
Posted By biofreak
Raw read counts per Exon

How do I obtain from the SAM/BAM file raw read counts per exon and not the gene?
thanks.
Forum: Bioinformatics 04-11-2012, 07:33 AM
Replies: 18
Views: 2,413
Posted By biofreak
oops! My bad :) thanks

oops! My bad :)
thanks
Forum: Bioinformatics 04-11-2012, 06:24 AM
Replies: 18
Views: 2,413
Posted By biofreak
I have specified separate output dir which shows...

I have specified separate output dir which shows all the 6 folders for the 6 lanes. Each one contains just the csv file for the respective sample but no zipped fastq files. My command is:

nohup...
Forum: Bioinformatics 04-11-2012, 06:02 AM
Replies: 18
Views: 2,413
Posted By biofreak
I am sorry for my lack of knowledge but I did...

I am sorry for my lack of knowledge but I did change the csv and it runs and does not output any fastq files.
The sample sheet now looks like.
...
Forum: Bioinformatics 04-11-2012, 05:44 AM
Replies: 18
Views: 2,413
Posted By biofreak
Oh thanks you so much. I'll make changes to my...

Oh thanks you so much. I'll make changes to my csv file for all the lanes.
I tried using casava to demultiplex the barcodes that I have (nugen) using --use-bases-mask field. It does not complain...
Forum: Bioinformatics 04-11-2012, 05:30 AM
Replies: 18
Views: 2,413
Posted By biofreak
Actually my samples do have Indexes which are not...

Actually my samples do have Indexes which are not Illumina. I want to convert the files to fastq and then use barsplitter ot something.
Forum: Bioinformatics 04-11-2012, 05:26 AM
Replies: 18
Views: 2,413
Posted By biofreak
thanks all. Here is the SampleSheet ...

thanks all. Here is the SampleSheet
FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
HHPDCAZX,1,H-1,Rat,,Hu,Control,HiSeq_R_90,Rob,Hu...
Forum: Bioinformatics 04-11-2012, 04:37 AM
Replies: 18
Views: 2,413
Posted By biofreak
noIndex in SampleSheet casava1.8

I simply want to convert .bcl files to .fastQ.
I am having trouble with SampleSheet.csv for casava1.8. My samples do not have index field and I kept the "index" field of the SampleSheet empty (as...
Forum: Bioinformatics 09-20-2011, 07:37 AM
Replies: 3
Views: 1,642
Posted By biofreak
Hi Simon, thanks a lot for the reply. I am...

Hi Simon,
thanks a lot for the reply.
I am sorry for the confusion.. I have 12 samples (4 groups with 3 replicates each). and I was comparing 2 groups each time.. So is there any way to not over...
Forum: Bioinformatics 09-16-2011, 10:33 AM
Replies: 3
Views: 1,642
Posted By biofreak
distribution of Pvalues in RNASeq data

Hi All,
I used DEseq package to find differentially expressed genes for my RNAseq data ( 2 conditions 3 samples each). I the plotted all the P values and the distribution is as follows (see...
Forum: Bioinformatics 08-11-2011, 10:49 AM
Replies: 1
Views: 1,755
Posted By biofreak
makeTranscriptDbFromUCSC

I have used the following command:
txdb <- makeTranscriptDbFromUCSC(genome = "canFam2", tablename = "refGene")
Does anyone know how to modify values in txdb object?
I want to change the chromosome...
Forum: Bioinformatics 08-11-2011, 09:02 AM
Replies: 0
Views: 1,160
Posted By biofreak
exonsBy function in GenomicRanges package

Hi All,
I am working with canFam2 data. The commands used are:
canFamrefGene <- makeTranscriptDbFromBiomart(biomart="ensembl",dataset="cfamiliaris_gene_ensembl")
exonRangesList <-...
Forum: Bioinformatics 08-08-2011, 10:35 AM
Replies: 0
Views: 695
Posted By biofreak
CanFam2 data RNAseq samples and GenomicRanges

hi All,
I am processing RNAseq samples for canFam2. I used the following commands from GenomicRanges package that gives me only 1218 genes. (because by default refGene for canFam2 retains only known...
Forum: Bioinformatics 08-03-2011, 09:56 AM
Replies: 6
Views: 4,283
Posted By biofreak
Hi Simon, I am using 1.4 version if DESeq. I...

Hi Simon,
I am using 1.4 version if DESeq. I tried filtering differentially expressed genes based on within group variance values from 'resVarA' and 'resVarB'. As you have mentioned, it is indeed...
Showing results 1 to 25 of 44

 


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