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Forum: Illumina/Solexa 07-20-2015, 11:31 AM
Replies: 6
Views: 2,615
Posted By upendra_35
Maximum insert size with Hiseq 3000

What is the maximum size of insert allowed/optimum in Hiseq 3000? For one of our analysis, we needed a longer insert size (~800bp) which is ok in the case of 2000 but i was told that it is not good...
Forum: Bioinformatics 11-25-2014, 06:27 PM
Replies: 0
Views: 776
Posted By upendra_35
Question: How to filter transcripts with overlapping exons?

When i was going through the bed file, i found that some of the entries define overlapping exons. One example is :

This is UCSC bed file format:

A01 5943412 5943616 Bra1000073 168 ...
Forum: RNA Sequencing 05-25-2014, 09:32 PM
Replies: 1
Views: 2,208
Posted By upendra_35
I don't know if it is too late for you but i...

I don't know if it is too late for you but i recently did something in the lines that you mentioned above - using RNA-Seq data to calculate Ka/Ks ratio for two genomes. For this first i have...
Forum: Bioinformatics 05-05-2014, 05:18 PM
Replies: 2
Views: 1,473
Posted By upendra_35
Hi, Did you figure out how to use the tool. I am...

Hi, Did you figure out how to use the tool. I am having hard time to use it as well...
Forum: RNA Sequencing 09-22-2013, 06:05 PM
Replies: 2
Views: 1,891
Posted By upendra_35
Hi chadn737, In the absence of these bam...

Hi chadn737,

In the absence of these bam files, is there any alternative exists to confirm our mutants before we start our anlaysis.

Thanks
Upendra
Forum: RNA Sequencing 09-22-2013, 12:28 PM
Replies: 2
Views: 1,891
Posted By upendra_35
How to add Arabidopsis T-DNA lines as tracks on IGV

Hi,
We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines (to make sure that we didn't mess...
Forum: Bioinformatics 04-09-2013, 11:39 PM
Replies: 10
Views: 3,219
Posted By upendra_35
My best guess would be ....Class code 'O'...

My best guess would be ....Class code 'O' transcripts you would be looking at.
Forum: Bioinformatics 01-30-2013, 01:35 PM
Replies: 1
Views: 1,721
Posted By upendra_35
Manual vs Blast2go annotation

I have recently finished my transcriptome assembly and currently in the process of annotating ~50k transcripts. For annotating, i thought of using two approaches....

Blasting those transcripts...
Forum: Bioinformatics 01-25-2013, 04:45 PM
Replies: 18
Views: 4,295
Posted By upendra_35
Thank you very much kmcarr, very useful tips....

Thank you very much kmcarr, very useful tips. Can't wait to start my Blast2Go annotation now. Thanks again.
Forum: Bioinformatics 01-24-2013, 11:13 PM
Replies: 18
Views: 4,295
Posted By upendra_35
Sorry my bad.....i have used pep file and not...

Sorry my bad.....i have used pep file and not cDNA file.
Forum: Bioinformatics 01-24-2013, 04:17 PM
Replies: 18
Views: 4,295
Posted By upendra_35
I got the same problem. When i tried to import...

I got the same problem. When i tried to import the xml file that was blatsted against Arabidopsis TAIR10 cDNA reference, the mapping and annotation steps failed in blast2go software. So i guess it is...
Forum: Bioinformatics 01-03-2013, 09:04 AM
Replies: 9
Views: 4,244
Posted By upendra_35
Could you tell me what option in blastclust would...

Could you tell me what option in blastclust would you use to output the consensus sequence? I searched all options but couldn't find one.

Thanks
Upendra
Forum: RNA Sequencing 11-29-2012, 01:09 PM
Replies: 6
Views: 6,185
Posted By upendra_35
Thanks for the hint. I got into the same problem...

Thanks for the hint. I got into the same problem as everyone above and your hint helped me to fix it. Thanks
Forum: Bioinformatics 11-18-2012, 09:16 AM
Replies: 0
Views: 870
Posted By upendra_35
edgeR query

Hi all,

For my experiment, I have three levels of factors for genotype ("B2, "Ein40","Ein9") and two levels of factors as treatment ("Sun", "Shade"). I did a nested interaction method in edgeR to...
Forum: Bioinformatics 11-15-2012, 09:51 PM
Replies: 1
Views: 2,159
Posted By upendra_35
USEARCH chimera removal memory error

Hi

I was trying to detect chimera removal command from USEARCH program and i have encountered memory related error. Does anybody have an idea of what it is.......and how to fix it?
...
Forum: Bioinformatics 11-15-2012, 11:36 AM
Replies: 9
Views: 4,244
Posted By upendra_35
Thanks for the info. Do you know what should be...

Thanks for the info. Do you know what should be the optimum value of i.d in USEARCH to be able to cluster the denovo transcripts generated by different assembler.
Forum: RNA Sequencing 11-09-2012, 12:24 PM
Replies: 38
Views: 16,913
Posted By upendra_35
Thanks. I have sent a PM to you........

Thanks. I have sent a PM to you........
Forum: RNA Sequencing 11-07-2012, 02:37 PM
Replies: 38
Views: 16,913
Posted By upendra_35
Hi I am just wondering have you fixed your...

Hi
I am just wondering have you fixed your script for paired end reads? I would like to try your script to extract the consensus sequences from bam file based on cufflinks gtf coordinates.
Forum: RNA Sequencing 10-30-2012, 04:02 PM
Replies: 0
Views: 710
Posted By upendra_35
Editing the reference sequence

I am interested in Reference based transcriptome assembly for my species of interest for which the reference sequence is available from a different accession. For reference based approach i used...
Forum: Bioinformatics 10-30-2012, 02:10 PM
Replies: 9
Views: 4,244
Posted By upendra_35
I don't know if you are still working on the...

I don't know if you are still working on the clustering but what i have done with my denovo transcripts that were generated from three different assembly algorithms is to cluster them using...
Forum: Academic/Non-Profit Jobs 10-24-2012, 11:04 PM
Replies: 6
Views: 1,780
Posted By upendra_35
Hi, I am from CA as well and though i am not...

Hi,

I am from CA as well and though i am not from Industry i have fair bit of RNAseq experience. I have done lots and lots of denovo and reference based assemblies and after undergoing through...
Forum: De novo discovery 10-23-2012, 05:19 PM
Replies: 11
Views: 6,014
Posted By upendra_35
Thanks for the info. Yes i did worked out on this...

Thanks for the info. Yes i did worked out on this a bit but in the manner that your colleague work. I have a feeling by myself that the Trinity transcripts are smaller when compared to known genes...
Forum: De novo discovery 10-23-2012, 05:15 PM
Replies: 11
Views: 6,014
Posted By upendra_35
Does that mean i should have more relaxed FPKM...

Does that mean i should have more relaxed FPKM cut-off? What do you think would be ideal by the way?
Forum: RNA Sequencing 10-23-2012, 07:17 AM
Replies: 2
Views: 1,754
Posted By upendra_35
Thanks Hobbe for the response. I just checked my...

Thanks Hobbe for the response. I just checked my fasta file and i could find the names in there. It does mean now that my gff is not complete. Do you know is there a way to get a complete gff...
Forum: RNA Sequencing 10-22-2012, 09:42 PM
Replies: 2
Views: 1,754
Posted By upendra_35
tophat junctions.bed file

I recently found that my junctions.bed file contained names that are not found in gff reference. How does it happen?

upendra_35@vm142-14 tophat_out_3_7_8_lanes]$ head junctions.bed
track...
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