Im currently analysing some mice samples and wanted to try the Ensembl annotation, I have only used UCSC before.
This is my tophat cmd:
tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bowtie2Index/genome 001.fastq.gz
this is my cufflinks cmd:
cufflinks --output-dir path/to --GTF-guide /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Archives/archive-2013-03-06-18-55-12/Genes/genes.gtf --frag-bias-correct /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bowtie2Index/genome.fa --multi-read-correct --upper-quartile-norm --verbose accepted_hits.bam
What worrying?
First:
20: MT
10: 18
11: 19
4: 12
5: 13
2: 10
3: 11
8: 16
9: 17
6: 14
7: 15
22: Y
21: X
19: 9
18: 8
17: 7
16: 6
15: 5
14: 4
13: 3
12: 2
1: 1
Does it seam correct for chromosome names?
Second, maybe 1000 warning like this:
GFF warning: merging adjacent/overlapping segments of ENSMUST00000101224 on 6 (84939386-84939418, 84939421-84939523)
What does that mean?
Third, what the meaning of:
Warning: intron not within scaffold ([102700571-102700733], 0)
Thank you very much!
This is my tophat cmd:
tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bowtie2Index/genome 001.fastq.gz
this is my cufflinks cmd:
cufflinks --output-dir path/to --GTF-guide /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Archives/archive-2013-03-06-18-55-12/Genes/genes.gtf --frag-bias-correct /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bowtie2Index/genome.fa --multi-read-correct --upper-quartile-norm --verbose accepted_hits.bam
What worrying?
First:
20: MT
10: 18
11: 19
4: 12
5: 13
2: 10
3: 11
8: 16
9: 17
6: 14
7: 15
22: Y
21: X
19: 9
18: 8
17: 7
16: 6
15: 5
14: 4
13: 3
12: 2
1: 1
Does it seam correct for chromosome names?
Second, maybe 1000 warning like this:
GFF warning: merging adjacent/overlapping segments of ENSMUST00000101224 on 6 (84939386-84939418, 84939421-84939523)
What does that mean?
Third, what the meaning of:
Warning: intron not within scaffold ([102700571-102700733], 0)
Thank you very much!
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