hi, Im newbie to linux and NGS. I have genome.fasta file and transcripts.gff3 file. Both files have different chromosome naming pattern due to which im unable to use them in cufflinks as its giving following error:
Warning: couldn't find fasta record for 'CA_chr13_BGI-A2_v1.0'! This contig will not be bias corrected.
can someone kindly help me how to equate chromosome naming in both files???
i mean the chromosome name for fasta file should exactly be the same as to that in gff3 file or vice versa. the chromosome names in the fasta file are as follows:
while in gff3 file these are as follows:
it would be more convenient if they are retained to simply as chr1, chr2,chr3 and so on rather than this long naming. further chr1 in fasta file should exactly be the chr1 in gff3 file.
kind help would be highly appreciated.