SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 8 of 8
Search took 0.00 seconds.
Search: Posts Made By: cpleis
Forum: Bioinformatics 07-30-2013, 08:21 AM
Replies: 8
Views: 10,958
Posted By cpleis
JP, Below is the format for the csv file that...

JP,
Below is the format for the csv file that corresponds to the heat map attached. I actually used SAS to get significant gene list, then calculated the log2-fold change. Then I took my...
Forum: Bioinformatics 01-18-2013, 07:15 AM
Replies: 8
Views: 10,958
Posted By cpleis
Hi SHeaph, Unfortunately I was not able to...

Hi SHeaph,
Unfortunately I was not able to resolve the issue. I think that the heat map function in R isn't able to resolved such a large number of data labels. I simply switched to showing the...
Forum: Bioinformatics 11-08-2012, 08:32 AM
Replies: 8
Views: 10,958
Posted By cpleis
Heatmap of RNA-Seq Data in R

Hello,
I have a large data set from RNA sequencing and I am trying to make a heatmap of my data. I have am having issues formatting my heatmap figure. My data set is large with the log2 fold...
Forum: Bioinformatics 10-15-2012, 09:31 AM
Replies: 8
Views: 3,465
Posted By cpleis
I re-did the alignment against the genome.

I re-did the alignment against the genome.
Forum: Bioinformatics 10-15-2012, 09:06 AM
Replies: 8
Views: 3,465
Posted By cpleis
Would a large number of isoforms not account for...

Would a large number of isoforms not account for the high number of ambiguous alignments? I was also going to try running my htseq-count alignment with a different mode. Currently I am using union,...
Forum: Bioinformatics 10-10-2012, 12:45 PM
Replies: 8
Views: 3,465
Posted By cpleis
Simon, It looks like my gff file does not...

Simon,
It looks like my gff file does not contain information about scaffold_785 and that is why reads mapping to scaffold_785 are skipped for counting. I'm assuming then that there is most likely...
Forum: Bioinformatics 10-10-2012, 09:50 AM
Replies: 8
Views: 3,465
Posted By cpleis
Simon, Thank you for your response. I re-did...

Simon,
Thank you for your response. I re-did the alignment using the complete nucleotide sequence (Gmax_109.fa) instead of the transcriptome using TopHat. I then sorted the accepted_hits.bam file...
Forum: Bioinformatics 10-08-2012, 01:44 PM
Replies: 8
Views: 3,465
Posted By cpleis
Issue with htseq-count

Hello,
I am working on an RNA-Seq project in soybean. I used Illumina HiSeq for single end reads on my soybean samples and am working on my alignment. I have run into a problem when trying to get...
Showing results 1 to 8 of 8

 


All times are GMT -8. The time now is 10:31 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO