Open rmenafra opened 3 years ago
There's expected to be some inflation but 19M doesn't make any sense..not even if you add all of them up.
Did you take a look at the all_samples.chained_ids.txt
? What does it look like? Can you show the first 20 lines? How many lines are in that file?
-Liz
all_samples.chained_ids.txt has 19766014 lines. The first 20 are below, I know that 19M makes no sense.
superPBID PC25 PC45 PC54 PC62 PC64 PC73 PB.1.1 NA PB.1.1 NA NA NA NA PB.2.1 NA NA NA NA PB.1.1 NA PB.2.2 NA NA NA NA PB.1.2 NA PB.3.1 PB.1.1 NA NA NA NA NA PB.3.2 NA NA PB.1.1 NA NA NA PB.3.3 NA NA NA NA PB.2.1 NA PB.4.1 NA PB.2.1 NA NA NA NA PB.4.2 PB.2.1 PB.2.2 NA NA PB.3.4 NA PB.4.3 NA PB.2.3 NA NA PB.3.1 NA PB.4.4 NA NA PB.2.3 PB.1.1 PB.3.2 NA PB.4.5 NA NA NA NA PB.3.3 NA PB.4.6 PB.2.2 NA NA NA PB.3.5 NA PB.4.7 NA NA PB.2.1 NA NA NA PB.4.8 NA NA NA PB.1.2 NA NA PB.4.9 PB.2.3 NA NA NA NA NA PB.4.10 NA NA PB.2.5 NA NA NA PB.4.11 PB.2.4 NA NA NA NA NA PB.4.12 PB.2.5 PB.2.5 NA PB.1.4 NA NA PB.4.13 PB.2.6 PB.2.4 PB.2.6 PB.1.3 PB.3.6 NA
Roberta
I'm having the same problem.
config file:
SAMPLE=Pool1_1;collapsed/Pool1_Suzy_1
SAMPLE=Pool2_2;collapsed/Pool2_Atrop_2
SAMPLE=Pool2_3;collapsed/Pool2_Bob_3
SAMPLE=Pool2_4;collapsed/Pool2_Tom_4
GROUP_FILENAME=sample.collapse_isoforms.collapsed.group.txt
GFF_FILENAME=sample.collapse_isoforms.collapsed.gff
COUNT_FILENAME=sample.collapse_isoforms.collapsed.abundance.txt
The initial number of transcripts after collapse is:
./Pool1_1/sample.collapse_isoforms.collapsed.gff
32441
./Pool2_3/sample.collapse_isoforms.collapsed.gff
39427
./Pool2_2/sample.collapse_isoforms.collapsed.gff
49306
./Pool2_4/sample.collapse_isoforms.collapsed.gff
12720
I installed cdna_cupcake v28.0.0 with conda and the command line is:
chain_samples.py config count_fl
The final number of transcripts in all_samples.chained.gff
is 2,189,160. Inspecting the GFF I saw many different transcripts ID with the same coordinates:
NC_051805.1 PacBio transcript 23876887 23917149 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23876887 23877711 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23881774 23881872 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23882552 23882622 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23889795 23889897 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23895117 23895259 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23897711 23897825 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23900552 23900665 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23900956 23901053 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23901373 23901482 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23903684 23903787 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23904276 23904437 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23905784 23905859 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23907966 23908115 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23910297 23910430 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio exon 23917054 23917149 . - . transcript_id "PB.489.1410"; gene_id "PB.489";
NC_051805.1 PacBio transcript 23876887 23917149 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23876887 23877711 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23881774 23881872 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23882552 23882622 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23889795 23889897 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23895117 23895259 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23897711 23897825 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23900552 23900665 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23900956 23901053 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23901373 23901482 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23903684 23903787 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23904276 23904437 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23905784 23905859 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23907966 23908115 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23910297 23910430 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio exon 23917054 23917149 . - . transcript_id "PB.489.1411"; gene_id "PB.489";
NC_051805.1 PacBio transcript 23876887 23917149 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23876887 23877711 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23881774 23881872 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23882552 23882622 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23889795 23889897 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23895117 23895259 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23897711 23897825 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23900552 23900665 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23900956 23901053 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23901373 23901482 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23903684 23903787 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23904276 23904437 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23905784 23905859 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23907966 23908115 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23910297 23910430 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
NC_051805.1 PacBio exon 23917054 23917149 . - . transcript_id "PB.489.1412"; gene_id "PB.489";
This specific gene PB.489
has 1,413 transcripts. but if I count only those with start and end equals and uniq I get 60 transcripts for this gene:
grep "\"PB.489\"" all_samples.chained.gff | awk '{print $1$2$3$4$5}' | sort | uniq | wc -l
I know that counting this way I could be losing some transcripts that have that same start and end because of the different exons usage, but as you can see in the example above, for the most part, shares identical exon usage.
Do you have some clue of how can I fix it?
Hi Liz, I'm using chain_samples.py on 6 human samples. The 6 samples were multiplexed and run over 6 SMRTcells and samples were combined after the refine step. After the collapse by isoform step the 6 samples had the following numbers of isoforms: 90465 134305 74215 84366 118929 109500 I used chain_samples with default parameters (in a clean folder) and obtained 19M isoforms. I was wondering if you have any idea of what could have happened. Thanks Roberta