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How to safely rename the chromosome names in fasta and gtf

I have a fasta with headers such like:

>chr1 1
>chr2 2
>chr3 3
>chr4 4
>chr5 5
>chr6 6
>chr7 7
>chr8 8
>chr9 9
>chr10 10
>chr11 11
>chr12 12
>chr13 13
>chr14 14
>chr15 15
>chr16 16
>chr17 17
>chr18 18
>chr19 19
>chrX X
>chrY Y
>chrM MT
>GL456210.1 GL456210.1
>GL456211.1 GL456211.1
>GL456212.1 GL456212.1
>GL456213.1 GL456213.1
>JH584292.1 JH584292.1
>JH584293.1 JH584293.1
>JH584294.1 JH584294.1
>JH584295.1 JH584295.1
>JH584296.1 JH584296.1

And in GTF 

chr1    HAVANA  gene    3073253 3074322 .       +       .       gene_id "ENSMUSG00000102693.1"; gene_type "TEC"; gene_name "4933401J01Rik"; level 2; havana_gene "OTTMUSG00000049935.1";
chr1    HAVANA  transcript      3073253 3074322 .       +       .       gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_name "4933401J01Rik"; transcript_type "TEC"; tr
chr1    HAVANA  exon    3073253 3074322 .       +       .       gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_name "4933401J01Rik"; transcript_type "TEC"; transcript
chr1    ENSEMBL gene    3102016 3102125 .       +       .       gene_id "ENSMUSG00000064842.1"; gene_type "snRNA"; gene_name "Gm26206"; level 3;
chr1    ENSEMBL transcript      3102016 3102125 .       +       .       gene_id "ENSMUSG00000064842.1"; transcript_id "ENSMUST00000082908.1"; gene_type "snRNA"; gene_name "Gm26206"; transcript_type "snRNA"; tran
chr1    ENSEMBL exon    3102016 3102125 .       +       .       gene_id "ENSMUSG00000064842.1"; transcript_id "ENSMUST00000082908.1"; gene_type "snRNA"; gene_name "Gm26206"; transcript_type "snRNA"; transcript_n
chr1    HAVANA  gene    3205901 3671498 .       -       .       gene_id "ENSMUSG00000051951.5"; gene_type "protein_coding"; gene_name "Xkr4"; level 2; havana_gene "OTTMUSG00000026353.2";

I wanted to add a letter "m" (denotes mouse) to these chromosome names such like mchr1 mchr2 etc.. How to safely do that?

rna-seq
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written by ddzhangzz ddzhangzz

for the fasta you can gsub >chr with >mchr and for the GTF simple print "m"$1, both with awk. Please use google for these simple text manipulation tasks. Still I recommend against it because this is not a standard notation and might cause trouble if you download other resources from the web (or at least requires additional preprocessing of everything you download like annotations etc.)

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written by ATpoint ATpoint

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