Closed BaluPai closed 6 years ago
Dear @BaluPai,
thank you for reporting your issue. Just to make sure we have everything that's required, are all of the *Aligned.sortedByCoord.out.bam
files indexed?
Also: -A /home/balupai/Annotations/STAR_hg38Genome/Genome
should be the original FASTA file of the employed genome. It looks you try to pass the STAR index?
Cheers, Tobias
Dear @tjakobi,
Yes I have made additional .bai files for all the *Aligned.sortedByCoord.out.bam files.
And regarding the Genome.fa and the index, yes I have a folder with all the .fa and the SAindex (STAR) file in there that I provide. Best, Balu
Dear @BaluPai,
thank you for your reply. What file is /home/balupai/Annotations/STAR_hg38Genome/Genome
exactly? -A
should be a FASTA file, not a directory or an index.
Something like -A /path/to/genome.fasta
Cheers, Tobias
Dear @tjakobi,
Yes it is a Fasta file...
Regards, Balu
Dear @BaluPai,
what samtools version are you currently using? You may have to generate a FASTA index first via samtools faidx /home/balupai/Annotations/STAR_hg38Genome/Genome
.
Cheers, Tobias
Dear @tjakobi, I guess it helped to Index the Genome.Fa separately again,And now it works all fine.
Thanks for the input. Cheers, Balu
DCC just hangs with no response at this step (counting the host gene expression)
_Started linear gene expression counting for /home/balupai/tools/DCC-0.4.6/DCC/joint-mapping/1_hg38Aligned.sortedByCoord.out.bam => running mpileup for start positions [/home/balupai/tools/DCC-0.4.6/DCC/joint-mapping/1_hg38Aligned.sortedByCoord.out.bam][faiload] build FASTA index.
And this is the command that I set for the DCC..
DCC @samplesheet.txt -mt1 @mate1.txt -mt2 @mate2.txt -D -R /home/balupai/Annotations/STAR_hg38Genome/Repeats_hg38_March2018.gtf -an /home/balupai/Annotations/STAR_hg38Genome/UCSC_hg38_knownGene_2017-08.gtf -Pi -F -M -Nr 5 2 -fg -G -A /home/balupai/Annotations/STAR_hg38Genome/Genome
Thanks in advance for any suggestions