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Search: Posts Made By: 4galaxy7
Forum: Bioinformatics 01-31-2017, 12:46 AM
Replies: 1
Views: 1,523
Posted By 4galaxy7
Normalising heatmap counts

I'm trying to produce a heatmap for my RNAseq dataset (using RPKM values). The counts vary from 5 - 40 000+. Obviously when I produce the heatmap, using Pheatmap, the values are very skewed towards...
Forum: Bioinformatics 01-26-2016, 09:55 AM
Replies: 0
Views: 1,021
Posted By 4galaxy7
calculating noise in gene expression from rna seq data set

hey, i've got an rna seq data set from 3 different conditions and i'm quite interesting in looking at the stochasticisity/noise between the conditions. has anyone come across any good software or...
Forum: Bioinformatics 01-14-2016, 03:41 AM
Replies: 1
Views: 2,840
Posted By 4galaxy7
WGCNA question - REAL() can only be applied to a 'numeric', not a 'integer'

Hi,

I'm tried to use the WGCNA bioconductor package on my RNAseq data - it was originally integer FPKM counts from the tuxedo pipeline, so I log2(x+1) transformed it (as was reccomended on the...
Forum: Bioinformatics 12-14-2015, 02:48 AM
Replies: 0
Views: 1,808
Posted By 4galaxy7
HTseq - count - high ambiguous count rate and reads with missing mate encountered

Hi. I'm using HTseq to produce some count read files that I can then use for NOIseq and edgeR. I used trimmomatic to trim my reads in paired end mode and merged the paired ends in tophat2 using
...
Forum: Bioinformatics 12-02-2015, 02:32 AM
Replies: 0
Views: 1,247
Posted By 4galaxy7
using cuffdiff files as an input for noiseq/edge r

hi,

i've put all my samples through cuffdiff (3 treatments, 7 samples in each treatment) and i also want to find differentially expressed genes from noiseq and edge r. I was struggling a bit with...
Forum: Bioinformatics 11-27-2015, 05:12 AM
Replies: 9
Views: 1,718
Posted By 4galaxy7
OK - tried that, but it comes up with an error...

OK - tried that, but it comes up with an error saying that there is different number of conditions..

user@IT060209:~$ /home/user/Downloads/cufflinks/cuffdiff -o /home/user/Desktop/cuffdiff_out/...
Forum: Bioinformatics 11-27-2015, 02:14 AM
Replies: 9
Views: 1,718
Posted By 4galaxy7
OK thanks! I'm a bit unclear about separating the...

OK thanks! I'm a bit unclear about separating the different conditions.

So with the L option, do you need to define the different conditions with a name that it then uses to check against the...
Forum: Bioinformatics 11-26-2015, 05:55 AM
Replies: 9
Views: 1,718
Posted By 4galaxy7
cuffdiff

hi,

so I'm slightly confused about the usage of cuffmerge/cuffdiff. as i see it, cuffmerge merges all of the .bam/.sam output files from tophat to produce a merged .gtf file which you then use as...
Forum: Bioinformatics 11-23-2015, 01:52 AM
Replies: 12
Views: 2,336
Posted By 4galaxy7
Yeah, I have the most recent version running. I...

Yeah, I have the most recent version running. I tried to change the PATH, but that didn't seem to work.

As a query, roughly sized files should I be expecting as the output of cufflinks/cuffmerge?...
Forum: Bioinformatics 11-18-2015, 06:05 AM
Replies: 12
Views: 2,336
Posted By 4galaxy7
user@IT060209:~$...

user@IT060209:~$ /home/user/Downloads/cufflinks/cuffmerge -v
merge_cuff_asms v1.0.0

user@IT060209:~$ /home/user/Downloads/cufflinks/cufflinks -v
cufflinks v2.2.1


That's what I tried...
Forum: Bioinformatics 11-18-2015, 05:55 AM
Replies: 12
Views: 2,336
Posted By 4galaxy7
Well it comes out with this... ...

Well it comes out with this...

user@IT060209:~/Downloads/cufflinks$ cuffmerge -o /home/user/Desktop/sam/cuffmerge_out -s /home/user/Downloads/DinoAntAssembly3.fna.1.fasta...
Forum: Bioinformatics 11-18-2015, 05:27 AM
Replies: 12
Views: 2,336
Posted By 4galaxy7
I downloaded the Linux binaries. ...

I downloaded the Linux binaries.

user@IT060209:~$ cufflinks -h
cufflinks: invalid option -- 'h'
cufflinks v2.1.1
Forum: Bioinformatics 11-18-2015, 04:49 AM
Replies: 12
Views: 2,336
Posted By 4galaxy7
BTW, any idea where the most recent version of...

BTW, any idea where the most recent version of cuffmerge is located? I just downloaded the most recent Cufflinks package from here http://cole-trapnell-lab.github.io/cufflinks/install/ - but when I...
Forum: Bioinformatics 11-18-2015, 03:47 AM
Replies: 12
Views: 2,336
Posted By 4galaxy7
Yeah sorry meant .gtf files! Perfect - that seems...

Yeah sorry meant .gtf files! Perfect - that seems easy. Thanks.
Forum: Bioinformatics 11-18-2015, 03:29 AM
Replies: 12
Views: 2,336
Posted By 4galaxy7
Cuffmerge question - manifest files

Hi,

So I'm new to using cuffmerge. I have all of my .bam files from the output of cufflinks and want to combine them using cuffmerge. I'm a bit confused about the command line usage of cuffmerge....
Forum: Bioinformatics 11-05-2015, 01:28 AM
Replies: 1
Views: 1,383
Posted By 4galaxy7
.gtf file issue - Error at parsing .tlst line (invalid strand):

I'm trying to align my reads to a genome + transcriptome, which is in the form of a .gtf file. It gets half way through and then runs this error:

user@it053392:~$ export...
Forum: Bioinformatics 11-03-2015, 05:50 AM
Replies: 5
Views: 2,469
Posted By 4galaxy7
OK. Sorry I know this is really basic, but when u...

OK. Sorry I know this is really basic, but when u say update your path - can this also mean copying the executable folders into the /bin folder? Cos on the TopHat site it says 'make sure the TopHat...
Forum: Bioinformatics 11-03-2015, 01:14 AM
Replies: 5
Views: 2,469
Posted By 4galaxy7
ok great thanks. im a bit of a noob with this, is...

ok great thanks. im a bit of a noob with this, is there a quick way to update the software without re-installing it? im in linux and tried sudo apt-get install but it is still running 2.0.0
Forum: Bioinformatics 11-02-2015, 09:07 AM
Replies: 5
Views: 2,469
Posted By 4galaxy7
EOF marker is absent - BAM file error in TopHat

Hi,

I've been running Bowtie with my RNAseq data, mapping the reads to the transcriptome (in .gtf format) and the genome.

I've kept getting an error which basically says:

user@it053392:~$...
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