annotateRangesWithTxDb function error

[ChoiJi-Hye]

Hi.

I follow vignette with my bam file.

However, When I entered annotateRangesWithTxDb (fds, txdb=txdb, orgDb=orgDb), i got warning and error message :
403 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object
Error in mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what=c("seqeunce", : sequence chrM has incompatible seqlengths:
- in 'x' : 16569
- in 'y' : 16571

I don't know what I can do with the fds object and how I can solve the problem.
Thank you for your help.

[aheritas]

Hi @c-mertes ,
I am having the same issue:

Error in mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",  : 
  sequence chrM has incompatible seqlengths:
  - in 'x': 16569
  - in 'y': 16571

My genome index was built using GRCh37.primary_assembly.genome.fa and gencode.v40lift37.annotation.gtf using the following:

STAR --runThreadN 10 --runMode genomeGenerate --genomeDir genome --genomeFastaFiles /data/genome/GRCh37.primary_assembly.genome.fa --sjdbGTFfile /data/genome/gencode.v40lift37.annotation.gtf --sjdbOverhang 100

My FASTQ (paired-end) were aligned to this index to obtain the BAMs used in FRASER using the following code:

STAR --genomeDir /data/blood/genome/genome --readFilesIn "$i"_1.fastq.gz "$i"_2.fastq.gz --runThreadN 16 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --chimSegmentMin 20 --quantMode GeneCounts --outReadsUnmapped Fastx --outFileNamePrefix ./star_out/"$i" --twopassMode Basic --outMultimapperOrder Random --sjdbGTFfile /data/blood/genome/gencode.v40lift37.annotation.gtf

Then, I followed the FRASER vignette but got to the same error as @ChoiJi-Hye . I am using Bioconductor version: Release (3.15).
I appreciate any feedback. Thank you.