User: Ziliang Luo

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Posts by Ziliang Luo

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Missing assembled transcripts after Stringtie merge
... 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 Luo0
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Comment: C: Missing assembled transcripts after Stringtie merge
... 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 Luo0
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Comment: C: Missing assembled transcripts after Stringtie merge
... 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 Luo0
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Missing assembled transcripts after Stringtie merge
... 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 ...
assembly stringtie rna-seq written 6 months ago by Ziliang Luo0
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Comment: C: How to do differential methylation analysis on huge WGBS data from plant?
... Thanks, I'll give it a try. ...
written 10 months ago by Ziliang Luo0
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How to do differential methylation analysis on huge WGBS data from plant?
... 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 ...
plant methylkit methylation wgbs sequencing written 10 months ago by Ziliang Luo0
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Comment: C: Sequence Bias Bismark Output Interpretation
... 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 Luo0
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Answer: A: miRDeep2 "no file 'precursors.fa_stack' found" error.
... 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 Luo0
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How to integrate mirdeep2 result from different samples
... 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 ...
mirdeep2 rna-seq mirna written 16 months ago by Ziliang Luo0

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Supporter 4 months ago, voted at least 25 times.

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