A quick question,
Do most people exclude the contigs and haplotype chromosomes from the Human genome (hg19) from their GTF annotation files for chromosome i.e.
GL000191.1
GL000192.1
GL000193.1
GL000194.1
GL000195.1
GL000197.1
GL000199.1
GL000200.1
GL000201.1
GL000204.1
GL000205.1
GL000209.1
GL000211.1
GL000212.1
GL000213.1
GL000214.1
GL000216.1
GL000218.1
GL000219.1
GL000220.1
GL000221.1
GL000222.1
GL000223.1
GL000224.1
GL000225.1
GL000227.1
GL000228.1
GL000229.1
GL000230.1
GL000233.1
GL000236.1
GL000237.1
GL000238.1
GL000239.1
GL000240.1
GL000241.1
GL000242.1
GL000243.1
GL000247.1
HSCHR17_1
HSCHR6_MHC_APD
HSCHR6_MHC_COX
HSCHR6_MHC_DBB
HSCHR6_MHC_MANN
HSCHR6_MHC_MCF
HSCHR6_MHC_QBL
HSCHR6_MHC_SSTO
If so why particularly if you are only interested in expression of genes? And why does the pre-built index for bowtie not contain contigs unplaced or unlocalized sequences and alternate haplotype
Do most people exclude the contigs and haplotype chromosomes from the Human genome (hg19) from their GTF annotation files for chromosome i.e.
GL000191.1
GL000192.1
GL000193.1
GL000194.1
GL000195.1
GL000197.1
GL000199.1
GL000200.1
GL000201.1
GL000204.1
GL000205.1
GL000209.1
GL000211.1
GL000212.1
GL000213.1
GL000214.1
GL000216.1
GL000218.1
GL000219.1
GL000220.1
GL000221.1
GL000222.1
GL000223.1
GL000224.1
GL000225.1
GL000227.1
GL000228.1
GL000229.1
GL000230.1
GL000233.1
GL000236.1
GL000237.1
GL000238.1
GL000239.1
GL000240.1
GL000241.1
GL000242.1
GL000243.1
GL000247.1
HSCHR17_1
HSCHR6_MHC_APD
HSCHR6_MHC_COX
HSCHR6_MHC_DBB
HSCHR6_MHC_MANN
HSCHR6_MHC_MCF
HSCHR6_MHC_QBL
HSCHR6_MHC_SSTO
If so why particularly if you are only interested in expression of genes? And why does the pre-built index for bowtie not contain contigs unplaced or unlocalized sequences and alternate haplotype
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