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Forum: Bioinformatics 08-09-2016, 02:16 AM
Replies: 1
Views: 2,260
Posted By dena.dinesh
Different alignment rate of Tophat with and without GTF file

Hi,

I am new to RNA seq analysis. I am working on non-model organism. I have Genome and de-novo-assembled transcriptome. Using PASA I mapped the transcriptome to genome and obtained GTF file.
...
Forum: Bioinformatics 08-14-2015, 05:54 AM
Replies: 1
Views: 1,708
Posted By dena.dinesh
Error: Invalid format for pileup at line null in varscan2

Hi,

I am using Varscan2 with readcounts like follows

samtools mpileup -f /home/tsekara/Transcriptomes/trinity5_frameDPcorrected.fa...
Forum: Bioinformatics 08-11-2015, 05:47 AM
Replies: 0
Views: 941
Posted By dena.dinesh
Counting the total number of SNPs in a transcript

Hi,

I have RNAseq data that has been aligned to reference transcriptome and the aligned bam file is sorted and indexed.

Using that bam file is it possible to estimate the total number SNPs in...
Forum: Bioinformatics 08-04-2015, 07:44 AM
Replies: 5
Views: 2,877
Posted By dena.dinesh
Hi Michael, The organism on which I work has...

Hi Michael,

The organism on which I work has no genome available so far so all I have to depend only on transcriptome for alignment.

I want to find the mutation from RNAseq data. So I mapped...
Forum: Bioinformatics 08-04-2015, 03:30 AM
Replies: 5
Views: 2,877
Posted By dena.dinesh
Hi Michael, I am new to RNAseq data...

Hi Michael,

I am new to RNAseq data analysis. I also want to obtain the complete sequence for every transcript that has been aligned from a bam file not just only consensus part. With the above is...
Forum: Bioinformatics 08-04-2015, 02:16 AM
Replies: 1
Views: 1,256
Posted By dena.dinesh
extracting complete sequence for every transcript from a bam file

hi,

I have bam obtained by aligning to a transcriptome. Is it possible to obtain the complete sequence that has been aligned to every transcript and make a fast file out aligned sequences for...
Forum: Bioinformatics 06-12-2015, 01:14 AM
Replies: 4
Views: 3,103
Posted By dena.dinesh
Thanks for your comment. In that case I think I...

Thanks for your comment. In that case I think I should use -Q33 parameter whevener I Clipp or trimm the sequence using fastx right? Kindly guide me
Forum: Bioinformatics 06-12-2015, 12:57 AM
Replies: 4
Views: 3,103
Posted By dena.dinesh
Is specifyng -Q33 in fastx_clipper for Sanger/Illumina1.9 encoding fastq important?

Hi,

I have fastq files which as Sanger/Illumina1.9 encoding. When I clipped off the linkers I havent specified the -Q33 but still it trimmed the linkers. As I didnt mention the Q33 parameter, is...
Forum: Bioinformatics 06-09-2015, 11:42 AM
Replies: 2
Views: 2,145
Posted By dena.dinesh
Thanks for your reply. So if I take correlation...

Thanks for your reply. So if I take correlation on vst transformed data or calculate the the Euclidean distances of vst data and perform hierarchical clustering the resulting dendograms should be the...
Forum: Bioinformatics 06-05-2015, 02:13 AM
Replies: 2
Views: 2,145
Posted By dena.dinesh
Finding the Similarity/dissimilarity of RNAseq samples using correlation

Hi,

I am working on RNAseq data for 8 samples which biological duplicates. I want to find how close the samples are with respect to each other. So I obtained the count data and loaded the file...
Forum: Bioinformatics 05-29-2015, 05:09 AM
Replies: 9
Views: 2,630
Posted By dena.dinesh
Hi, I just uninstalled that older version...

Hi,

I just uninstalled that older version and re installed the newer version. Now bowtiw has 2.2.5. Now I ma finidng difficult to interpret the results os sam/bam alignment file. When I dont...
Forum: Bioinformatics 05-29-2015, 03:50 AM
Replies: 9
Views: 2,630
Posted By dena.dinesh
Here is a full SAM record for particular...

Here is a full SAM record for particular transcript
...
Forum: Bioinformatics 05-29-2015, 03:35 AM
Replies: 9
Views: 2,630
Posted By dena.dinesh
Hi Ryan, My doubt is that when the seed...

Hi Ryan,

My doubt is that when the seed length is 25 and I havent allowed any mismatches, then how could there be Read Sequences in my bam/sam file which are less than 25. Am I missing something....
Forum: Bioinformatics 05-29-2015, 02:41 AM
Replies: 9
Views: 2,630
Posted By dena.dinesh
Thanks for your reply. I read the article. In my...

Thanks for your reply. I read the article. In my case, as I ran Bowtie2 with default parameters(Seed length 25 and no mismatch). Now when there is 12M in Cigar and Read Sequence like ATGGCAGTGTTG,...
Forum: Bioinformatics 05-29-2015, 01:22 AM
Replies: 9
Views: 2,630
Posted By dena.dinesh
Interpreting the CIGAR and Read Sequence in sam/bam

Hi,

I ran bowtie2 to align the fastq reads to align against a de novo assembled transcriptome. I ran the following command.

bowtie2 -p 30 /path/to/bowti2_indexes -U Sample1.fastq -S...
Forum: Bioinformatics 03-31-2015, 05:22 AM
Replies: 6
Views: 2,535
Posted By dena.dinesh
I am trying to install BLAT but somehow it throws...

I am trying to install BLAT but somehow it throws error when I use "make" command amd I am currently finding th solution for it. Is there any alternative way to address my question. Kindly guide me
Forum: Bioinformatics 03-31-2015, 04:43 AM
Replies: 6
Views: 2,535
Posted By dena.dinesh
Did you meant BLAST?

Did you meant BLAST?
Forum: Bioinformatics 03-31-2015, 04:14 AM
Replies: 6
Views: 2,535
Posted By dena.dinesh
Comparing Transcriptomes and finding common transcript IDs

Hi,

I have two transcriptomes, Transcriptome_old and Transcriptome_new both generated using de novo approach at different time point with different lengths. Now I would compare these these...
Forum: RNA Sequencing 03-27-2015, 06:03 AM
Replies: 3
Views: 3,010
Posted By dena.dinesh
Thanks Genomax. What do you mean by source files...

Thanks Genomax. What do you mean by source files are not compressed? These were just fastq files and not associated with any zip or tar.
Forum: RNA Sequencing 03-27-2015, 05:54 AM
Replies: 3
Views: 3,010
Posted By dena.dinesh
Combinig technical fastq files into a single fastq file

Hi,

I have technical replicate fastq files for some samples. For an example I have technical replicates like control_1a.fastq and control_1b.fastq. I would like to combine these two replicates as...
Forum: Bioinformatics 02-25-2015, 11:55 AM
Replies: 12
Views: 4,036
Posted By dena.dinesh
I tried the above command but it stiil shows...

I tried the above command but it stiil shows syntax error
Forum: Bioinformatics 02-25-2015, 11:44 AM
Replies: 12
Views: 4,036
Posted By dena.dinesh
No. I didnt modify any command. i just ran after...

No. I didnt modify any command. i just ran after saving the link. What has to modified?
Forum: Bioinformatics 02-25-2015, 11:38 AM
Replies: 12
Views: 4,036
Posted By dena.dinesh
Hi Genomax, I tried exactly what you said,...

Hi Genomax,

I tried exactly what you said, but it throwed me an error as I stated above
Forum: Bioinformatics 02-25-2015, 11:27 AM
Replies: 12
Views: 4,036
Posted By dena.dinesh
Hi Maubp, You mean to say that I have to...

Hi Maubp,

You mean to say that I have to copy the code from the plain text to a editor and save it as a pythin script and later run it as python program? Am I right?
Forum: Bioinformatics 02-25-2015, 07:02 AM
Replies: 12
Views: 4,036
Posted By dena.dinesh
Hi genomax, I downloaded the the python...

Hi genomax,

I downloaded the the python script and corresponding xml files from the GitHub by right clicking it and the saved the link as it is. Later I installed Biopython.
But when i ran the...
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