REFERENCE GENOME - merging files
Hi!
I would like to create a new reference genome (host + other genes) for mapping transcriptomic data
In order to do this, I have the 2 .fa files and the 2 .gtf files
For fasta files, I can easly merge the files cat file1.fa file2.fa > file1.2.fa
And for gtf files? What can I do?
Thanks for the help
• 2,608 views
•
link
written
by
GiuliaAC •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Expanding reference genome with alt loci and decoy sequences
written by appropiate •
-
How to run pal2nal on many files?
written by cats123 •
-
Size of Output BAM file bigger than the SUM Size of Input files after merging with samtools
written by Giggle •
-
Align two fasta files against each other
written by Palgrave •
-
Do STAR genome index and RSEM reference need to be from same files?
written by prabin.dm
-
Join/Combine gff3 or gtf files
written by deshpande.neha2 •
-
Obtain sequences that did not appear in your fasta file
written by sicat.paolo20 •
-
Concatenate the chromosome files from hsa19 into a single FASTA file
written by Kato •
-
linux 'cat' command merge fasta files without headers
written by esterbuiate •
-
How To Merge Two Fastq.Gz Files?
written by newDNASeqer
(cat f1.gtf && grep -v "^#" f2.gtf) > 1.2.gtf?to extend this, it could be as simply concat both files, just be sure you have different chromosome names
How can I check it? And if they are not different, what can I do?
May be best to use
agat_sp_merge_annotations.plfrom AGAT a proper GTF/GFF tooklit.I didn't know AGAT, thank you!