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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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Problem during host gene expression counting #51

Closed BaluPai closed 6 years ago

BaluPai commented 6 years ago

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

tjakobi commented 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

BaluPai commented 6 years ago

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

tjakobi commented 6 years ago

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

BaluPai commented 6 years ago

Dear @tjakobi,

Yes it is a Fasta file...

Regards, Balu

tjakobi commented 6 years ago

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

BaluPai commented 6 years ago

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