Tobias Neumann comments

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                                            Tobias Neumann

Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

Does wildcard not work? like `*/*/*fq.gz`?

Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

Is the process itself also stuck or still running? What does `top` say, does it still use CPU?

Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

Hi - do you have 20GB per file or in total? It shouldnt really run much longer than 1 hour per file, so for sure be done within 24 hours

Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

Hi - that indeed sounds unreasonably slow. What command did you use, what's your memory size and did you make sure that NextGenMap is running with 16 cores (e.g. with...

Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

OH sorry now I think I see what's going on. it seems to be running with only 1 core per process. What happens if you do `-t 256` and then...

Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

Yes try `slamdunk all -r hg19.fa -b Hg.bed -o output -t 256 -rl 100 -ss data/*.fq.gz` `

Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

What does the CPU utilization in `top` say? You can increase the number of threads, just at some point the communication overhead outweighs the gain in speed

3'UTR length

Hi - 3' end sequencing only amplifies the last ~250bp of each transcript. So our annotations does a couple of processing steps to tailor the annotation to 3' end sequencing....

3'UTR length

Hi @Choopanian-Peyman - which annotation file do you use? It could be there are multiple counting windows (one for each isoform) reported thats why you will have several entries per...

Use slamdunk -all get the filter dicrectory "_mapped_filtered.bam " file just 8kb?

Hi - are there any reads in the bam file or none at all? What does `samtools flagstat DMSO_8h_trim_rep1.fq_slamdunk_mapped_filtered.bam` tell you?