I use the AIDE like the follow, and I didn't use the argument "genes":
aide(gtf_path = "../combine.gtf",
bam_path = "../bam_GRCH38/outprefix_GRCH38Aligned.sortedByCoord.out.bam",
fasta_path = "../genome.fa",
out_dir = "./",
readLen = 76,
strandmode = 0,
ncores = 30
)
but the AIDE stay the step of "reconstructing transcripts ..." for a too long time, it always output the follow for about ten days, then it output the result of transcript.gtf finally:
[1] "gene: 101"
[1] "gene: 102"
[1] "gene: 65"
[1] "gene: 79"
[1] "gene: 90"
[1] "gene: 81"
[1] "gene: 107"
[1] "gene: 111"
[1] "gene: 105"
[1] "gene: 62"
[1] "gene: 131"
[1] "gene: 132"
so can you tell me some ideas to solve the reason that AIDE stays in this step too long time ? or some problems about my parameters. thanks a lot.
I use the AIDE like the follow, and I didn't use the argument "genes": aide(gtf_path = "../combine.gtf", bam_path = "../bam_GRCH38/outprefix_GRCH38Aligned.sortedByCoord.out.bam", fasta_path = "../genome.fa", out_dir = "./", readLen = 76, strandmode = 0, ncores = 30 )
but the AIDE stay the step of "reconstructing transcripts ..." for a too long time, it always output the follow for about ten days, then it output the result of transcript.gtf finally: [1] "gene: 101" [1] "gene: 102" [1] "gene: 65" [1] "gene: 79" [1] "gene: 90" [1] "gene: 81" [1] "gene: 107" [1] "gene: 111" [1] "gene: 105" [1] "gene: 62" [1] "gene: 131" [1] "gene: 132"
so can you tell me some ideas to solve the reason that AIDE stays in this step too long time ? or some problems about my parameters. thanks a lot.