Question: running MISO with ENSEMBL GTF if reads were aligned against UCSC genome
0
gravatar for lavanya.kannan
2.2 years ago by
lavanya.kannan0 wrote:

I aligned reads against UCSC genome using STAR, where UCSC gtf was used as reference annotation. As a result, I get the chromosomes in the format "chr1", .... When using pe-utils function in MISO, it is identifying 0 read pairs. I get this error when I tried using both Homo_sapiens.GRCh37.65.gff and hg19_ensGene.gff3 annotation files and also tried the --no-bam-filter option of the pe-utils function. I notice that my bam files also have "chrM". Will removing reads from "chrM" help?

rna-seq miso • 862 views
ADD COMMENTlink modified 2.2 years ago by Emily_Ensembl18k • written 2.2 years ago by lavanya.kannan0
1
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

Why not just fix the chromosome names?

  1. samtools view -H foo.bam > header
  2. Edit the header (mostly, remove "chr" and convert "chrM" -> "MT")
  3. samtools reheader
ADD COMMENTlink written 2.2 years ago by Devon Ryan91k

Devon, worked now. Thanks for the suggestion.

ADD REPLYlink written 2.2 years ago by lavanya.kannan0
0
gravatar for Emily_Ensembl
2.2 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

You can use the Ensembl File Chameleon to export an Ensembl annotation file with "chr" style names.

ADD COMMENTlink written 2.2 years ago by Emily_Ensembl18k

That's an interesting tool. Does it have the name conversions stored somewhere or does it just tack on chr everywhere?

ADD REPLYlink written 2.2 years ago by Devon Ryan91k
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