I am very new to RNA-Seq. I am trying to align my samples with STAR. I am generating the genome index myself. Because I was hoping to add the spike-in sequence to the GTF and FASTA files.
I am downloading the GTF file from here: ftp://ftp.ensembl.org/pub/release-86/gtf/mus_musculus/
There are 2 GTF files one with CHR in the name and one without. I was wondering which one should I use and how they are different. I have not figured this out just by opening the files.
Thank you,
If you are not sure too, would you please let me know which one you use for your analysis.
The one with CHR seems to have more lines and it seems to be scaffold genes. Am I missing something?
2 answers
The one without 'chr' contains annotations for genes on unplaced or unlocalized contigs, while the one with 'chr' only contains annotation for assembled chromosomes, both of them have no prefix 'chr' in chromosome name, see this example:
zcat Danio_rerio.GRCz10.87.gtf.gz | cut -f1 | awk '{dict[$1]++}END{for(i in dict) print i, dict[i]}'
KN150307.1 9
KN150451.1 7
KN150002.1 3
KN149765.1 3
KN149909.1 15
KN149998.1 13
#!genebuild-last-updated 1
KN150027.1 10
KN149917.1 7
KN150188.1 24
...
13 43069
20 48282
KN150399.1 11
KN150221.1 10
KN150670.1 32
KN149696.1 225
21 40566
...
zcat Danio_rerio.GRCz10.87.chr.gtf.gz | cut -f1 | awk '{dict[$1]++}END{for(i in dict) print i, dict[i]}' | head
#!genebuild-last-updated 1
MT 147
#!genome-date 1
10 40589
11 40971
12 39371
13 43069
20 48282
21 40566
14 35910
So which one should be used?
I am carrying out analysis in Homo sapiens and am doing a differential expression analysis of RNA-seq data.
Could you provide a link to the correct response? I have been struggling in my variant analysis as my initial GTF was with 1,2,.. as the chromosome names whereas later in the downstream analysis many files have the contigs as chr1, chr2,.... So, I don't know what to do!
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They're the same, just one doesn't have the prefix. I often use the one without the 'chr' prefix, and when references needed to be mixed with those downloaded from the UCSC genome browser, I remove the prefix manually.
thank you very much
I don't think this is accurate. OP was referring to the presence or absence of
chrin the file name, not the contig names. Please see A: Difference between GTF file with CHR and without CHR. ENSEMBL