Has anyone else noticed that the GTF files in the Illumina iGenomes collection don't conform to the GTF specification ? The attribute list must begin with gene_id then transcript_id whereas in the iGenomes GTFs it is gene_id then gene_name then either p_id or transcript_id. It would be nice if those extra attributes were at the end of the list so they worked with more programs.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Yeah, well Illumina has always been known about going off on their own. In any case I question a program that can not parse an arbitrary field. If the order of the attribute list *must* be in a given order then the specification should have just made room for two more exact columns instead of relying on programs to do the parsing.
-
Comment
-
Originally posted by fongchun View Post
Do you also get 0 FPKM when you use the GRCh37 from the Tophat site?
Comment
-
Yes. I tried both the iGenome GRCh37 packages downloaded from Tophat and Cufflinks and both genes.gtf file gave me 0 FPKM for all genes when I just used cufflinks with the -G parameter.
It seems that maybe the current archive version (archive-2011-08-30-22-38-04) doesn't work? Anyone else have problems?
Comment
-
It took me a week to drill back through my pipeline and work out these files were messing it up. In the end I got a fresh genome and GTF from ensembl, then used custom scripts to build all the various files req'd for picard, GATK etc. Its now working like a dream.
Lesson - if it looks too good to be true...@sidderb
Comment
-
Originally posted by sidderb View PostIt took me a week to drill back through my pipeline and work out these files were messing it up. In the end I got a fresh genome and GTF from ensembl, then used custom scripts to build all the various files req'd for picard, GATK etc. Its now working like a dream.
Lesson - if it looks too good to be true...
Lesson - check to see if "chr" is appended to the chromosome number or not when dealing with datasets.
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 08:47 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
54 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
Comment