I use IGV to view BAM files. Most times I'm viewing single chromosome genomes. When view single chromosomes I'm able to view annotations by making a .genome using a fasta and gff file. However on occasions I need to view 2 chromosomes in a single BAM. These BAM files have been made using a reference genome where the 2 fasta files have been concatenated into a single file. I've tried making a .genome in IGV with concatenated fasta and gff files, but the annotations for the first chromosome does not show for the first 100,000 bases. Fasta and gff files being used are ref_seq, so the formatting of theses files should be correct.
Something is wrong with how I'm inputting the annotated files. Is there a proper way of showing annotations for multiple chromosomes in IGV?
•
written
by
yellowbike •
0 answers
No answers yet.
Log in to answer this question.
-
IGV: first bases of each chromosomes missing when loading genome file
written by Pierre •
-
Why higher read counts in chromosome M/MT
written by Lou11 •
-
Cannot Modify Fasta File description
written by bkffadia •
-
Inputs required for CNVnator
written by sjlee4019 •
-
samtools view extract from .bed list to .bam file
written by matthews.alix •
-
How to subset bamfile based on chromosome IDs
written by mernster •
-
How to load BAM files that do not have chromosome name in the header?
written by JC •
-
Changing Chromosome Notation in Bam Files to Include Sample ID
written by dthorbur
-
Matching BAM and FASTA files for S. Cerevisiae
written by AlchemistMoz •
-
Rtracklayer: Converting rlelist (Coverage) to bigwig
written by datascientist28
