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:

gnl|BGIA2|CA_chr1

gnl|BGIA2|CA_chr2

while in gff3 file these are as follows:

CA_chr4_BGI-A2_v1.0

CA_chr6_BGI-A2_v1.0

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.

thanks 

Try this and let me know (assuming that file has # before headers): 

    $ awk  '!/#/ {split($1, a, "_"); $1=a[2]}1'  OFS='\t' test.gtf

input gtf:

    $ cat test.gtf 
    ##gff-version	null
    CA_chr4_BGI-A2_v1.0	GLEAN	mRNA	123284514	123288477	0.999991-	.	ID=Cotton_A_18927_BGI-A2_v1.0;Name=Cotton_A_18927;source_id=CottonA_GLEAN_10022228;identical_support_id=CUFF67.1103.1;evid_id=Cot030308.1
    CA_chr4_BGI-A2_v1.0	GLEAN	CDS	123288376	123288477	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    CA_chr4_BGI-A2_v1.0	GLEAN	CDS	123287662	123287826	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    CA_chr4_BGI-A2_v1.0	GLEAN	CDS	123287427	123287536	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    CA_chr4_BGI-A2_v1.0	GLEAN	CDS	123287129	123287237	.	-1	Parent=Cotton_A_18927_BGI-A2_v1.0
    CA_chr4_BGI-A2_v1.0	TEMP	CDS	123286939	123287051	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    CA_chr4_BGI-A2_v1.0	OUT	CDS	123286180	123286330	.	-1	Parent=Cotton_A_18927_BGI-A2_v1.0
    CA_chr4_BGI-A2_v1.0	NYCTY	CDS	123284514	123285671	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    CA_chr9_BGI-A2_v1.0	GLEAN	mRNA	17802711	17803334	1	+.	ID=Cotton_A_16149_BGI-A2_v1.0;Name=Cotton_A_16149;source_id=CottonA_GLEAN_10030787;evid_id=Cot023903.1

output gtf:

    $ awk  '!/#/ {split($1, a, "_"); $1=a[2]}1'  OFS='\t' test.gtf
    ##gff-version	null
    chr4	GLEAN	mRNA	123284514	123288477	0.999991-	.	ID=Cotton_A_18927_BGI-A2_v1.0;Name=Cotton_A_18927;source_id=CottonA_GLEAN_10022228;identical_support_id=CUFF67.1103.1;evid_id=Cot030308.1
    chr4	GLEAN	CDS	123288376	123288477	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    chr4	GLEAN	CDS	123287662	123287826	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    chr4	GLEAN	CDS	123287427	123287536	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    chr4	GLEAN	CDS	123287129	123287237	.	-1	Parent=Cotton_A_18927_BGI-A2_v1.0
    chr4	TEMP	CDS	123286939	123287051	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    chr4	OUT	CDS	123286180	123286330	.	-1	Parent=Cotton_A_18927_BGI-A2_v1.0
    chr4	NYCTY	CDS	123284514	123285671	.	-0	Parent=Cotton_A_18927_BGI-A2_v1.0
    chr9	GLEAN	mRNA	17802711	17803334	1	+.	ID=Cotton_A_16149_BGI-A2_v1.0;Name=Cotton_A_16149;source_id=CottonA_GLEAN_10030787;evid_id=Cot023903.1

