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Search: Posts Made By: jake13
Forum: Bioinformatics 02-26-2015, 02:31 PM
Replies: 5
Views: 4,178
Posted By jake13
StringTie software?

I saw this in the latest issue of nature biotech: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3122.html. Here is the site for it: http://ccb.jhu.edu/software/stringtie/. Has anyone used...
Forum: Bioinformatics 01-19-2015, 03:35 PM
Replies: 0
Views: 1,008
Posted By jake13
Cuffnorm no cds or tss

I am trying to use cuffnorm after tophat and cuffquant. I am using the gencodevM3 annotation and have filtered it so that it only contains CDS and exon information. However, when I run cuffnorm on my...
Forum: Bioinformatics 12-03-2014, 10:35 AM
Replies: 2
Views: 1,549
Posted By jake13
help with DaPars

I'm trying to use the DaPars package (http://dldcc-web.brc.bcm.edu/lilab/zheng/DaPars_Documentation/html/DaPars.html) and had a few questions.

First for the BED file, there are several options...
Forum: Bioinformatics 12-03-2014, 12:22 AM
Replies: 4
Views: 4,504
Posted By jake13
I'm having the same issue if anyone has a...

I'm having the same issue if anyone has a solution?
Forum: Bioinformatics 10-14-2014, 10:04 PM
Replies: 3
Views: 2,254
Posted By jake13
Analysis pipeline tools: make? bpipe? snakemike

I'm interested in putting some of my analysis into an easy to run pipeline. It seems like a make file is the way to go. However, it seems like people have written a number of tools such as snakemake...
Forum: Bioinformatics 05-08-2014, 03:01 PM
Replies: 0
Views: 892
Posted By jake13
cuffdiff fewer isoform than gene changes

I've been using cuffdiff and cummeRbund to analyze my RNA-seq data. When I use the getSig function with level="genes", I get 1869 genes that are different between my two samples. However, when I do...
Forum: Bioinformatics 04-14-2014, 03:13 PM
Replies: 1
Views: 1,274
Posted By jake13
problem with merged gtf in cuffdiff

Mixed up some filenames. Solved.
Forum: Bioinformatics 03-24-2014, 10:18 AM
Replies: 3
Views: 1,313
Posted By jake13
I first ran cufflinks on each sample with the...

I first ran cufflinks on each sample with the following command:
cufflinks -p 16 -u -g $gencode_gtf -b $gencode_fasta -M $gencode_rRNA --library-type fr-firststrand sample1.bam

cufflinks -p 16 -u...
Forum: Bioinformatics 03-23-2014, 07:04 PM
Replies: 3
Views: 1,313
Posted By jake13
reference transcripts missing after cuffmerge

I ran cufflinks on my rna-seq samples and then ran cuffmerge with the -g (reference gtf) and -s (reference sequence) options, which I thought would merge all of the reference transcripts with my...
Forum: Bioinformatics 03-13-2014, 11:52 PM
Replies: 0
Views: 1,059
Posted By jake13
problem with gffread and exon_number

I ran cufflinks to find novel transcripts on my RNA-seq samples and want to run cuffdiff. However, I want to first filter out any novel single exon transcripts before running cuffmerge. I have been...
Forum: Bioinformatics 03-03-2014, 10:14 PM
Replies: 5
Views: 2,460
Posted By jake13
cufflinks filter output gtf

I have been running cufflinks on a number of RNA-seq files to find novel transcripts/isoforms. I sequenced fairly deeply and it seems to be calling a ton of novel, short, single exon transcripts, a...
Forum: Bioinformatics 02-27-2014, 06:36 PM
Replies: 3
Views: 1,762
Posted By jake13
Cuffdiff stranded and unstranded data

I have generated stranded RNA-seq data and have been comparing it using cuffdiff. However, I now want to compare some of my samples to a previously published data set that does not have stranded...
Forum: Bioinformatics 01-23-2014, 08:07 PM
Replies: 2
Views: 1,310
Posted By jake13
An update for anyone else running into this...

An update for anyone else running into this problem. It seems to be caused by the gtf file that I was using. I tried grabbing the refseq gtf file from the UCSC table browser as well as the genes.gtf...
Forum: Bioinformatics 01-19-2014, 01:59 PM
Replies: 2
Views: 1,310
Posted By jake13
cuffdiff dispersion cutting off low values

I've been running cuffdiff on some paired end rna seq samples with biological replicates. Before I started analyzing them I checked the dispersion plots using cummeRbund. For some reason it is...
Forum: Bioinformatics 01-10-2014, 02:52 PM
Replies: 12
Views: 3,267
Posted By jake13
So someone else suggested I try an older version...

So someone else suggested I try an older version of tophat. I ran my files with 2.0.8b and 2.0.9 and everything ran fine so I guess I will just use that.
Forum: Bioinformatics 01-10-2014, 11:01 AM
Replies: 12
Views: 3,267
Posted By jake13
So I tried that and it did not fix the problem....

So I tried that and it did not fix the problem. Right now my sample is split into multiple fastq.gz files so I tried running each file separately. All of them ran fine except for one pair, which...
Forum: Bioinformatics 01-09-2014, 07:54 PM
Replies: 12
Views: 3,267
Posted By jake13
Thanks, took a look at that, but I'm not sure...

Thanks, took a look at that, but I'm not sure where to make those edits.
Forum: Bioinformatics 01-09-2014, 06:57 PM
Replies: 12
Views: 3,267
Posted By jake13
I tried resume and it didn't work, but I'm...

I tried resume and it didn't work, but I'm retrying with more memory. The --no-discordant option shows up for tophat in the run log, but not for tophat_reports.
Forum: Bioinformatics 01-09-2014, 06:33 PM
Replies: 12
Views: 3,267
Posted By jake13
Sorry I run tophat2 with the --no-discordant...

Sorry I run tophat2 with the --no-discordant option, but it seems to fail when it has to call tophat_reports.
Forum: Bioinformatics 01-08-2014, 08:08 AM
Replies: 12
Views: 3,267
Posted By jake13
tophat fails with --no-discordant

I'm trying to run tophat2.0.10 on some PE RNA-seq samples. However, tophat_reports fails at the reporting output tracks step with the error below. If I run tophat without the --no-discordant option...
Forum: Bioinformatics 10-27-2013, 11:55 AM
Replies: 0
Views: 1,005
Posted By jake13
Mapping with pseudogenes

I've searched a bit, but haven't found a great answer. How does mapping software such as Tophat2 take into account genes which have a processed pseudogene with over 90% sequence identity?
thanks
Forum: Bioinformatics 09-11-2013, 08:39 PM
Replies: 3
Views: 2,175
Posted By jake13
Check that replicates are good

Hi,
I'm new to RNA-seq analysis. I have biological duplicates of 4 different conditions. I want to check how good the replicates are for each condition. I have got them mapped to the genome and have...
Forum: Bioinformatics 08-29-2013, 05:41 PM
Replies: 1
Views: 1,787
Posted By jake13
cummeRbund MDS/PCA gene list

Hi,
I've run both the MDSplot and PCAplot on some data in cummeRbund. I was wondering if it is possible to get the list of genes that are contributing to PC1 and PC2?
Thanks.
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