User: Ziliang Luo
Ziliang Luo • 0
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Posts by Ziliang Luo
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... I'm not sure what's the issue here, you can contact the developer for this problem. Or just use de novo assembly. ...
written 4 months ago by
Ziliang Luo • 0
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... Seems that Stringtie use reference annotation as the gold standard. I used an improved annotation file where my interested genes are correctly annotated, and the merging step worked with that file. You can try the newest Stringtie2 to test if it works or use other de novo assembly approach (such as ...
written 5 months ago by
Ziliang Luo • 0
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... Hi Kristoffer,
The -i option didn't improve the result. I also notice that some samples assembled 2 separate fragments of this single exon gene. Maybe this inconsistency among samples "confuses" the stringtie?
Besides, seems thhe Stringtie strictly follows the provided reference. By using a update ...
written 6 months ago by
Ziliang Luo • 0
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... Hello,
I'm using Stringtie v2.0.4 for my RNAseq data analysis. I have a reference genome and annotation file but I still want to identify novel genes since the annotation is not complete for my species. I used:
for f in *.bam;
do
echo ${f};
stringtie -p 8 -f 0.3 -j 5 -G g ...
written 6 months ago by
Ziliang Luo • 0
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... Thanks, I'll give it a try. ...
written 10 months ago by
Ziliang Luo • 0
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... Hello,
I have a WGBS data from plant species. (2 treatments and 1 control with 3 replicates each). I aligned my data to genome using Bismark and extracted the methylation information using MethylDackel. I'm also intereated in CHH and CHG sites so I used `--CHG --CHH`. But I find that the CHH files ...
written 10 months ago by
Ziliang Luo • 0
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... Hi Kramdi,
Thanks for the clarification. What I don't understand is why the CpG methylation seems normal for reads 2, if the drop of other methylations (CHH CHG) is due to the overlap and therefore not called. ...
written 12 months ago by
Ziliang Luo • 0
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... before "precursors.fa_stack found" error came out and killed the program. it reported excision of precursor at certain iteration.
e.g
#excising precursors
...
46 217072
47 210636
48 204216
49 198362
No file mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.fa_stack ...
written 16 months ago by
Ziliang Luo • 0
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... Hello,
I'm using mirdeep2 to analyze my small RNA seq data (50 bp). I followed their tutorial for the analysis:https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md. I analyzed each sample separately and get the result output for each sample.
for f in \*clp.fa;do echo ${f}; miRDe ...
written 16 months ago by
Ziliang Luo • 0
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