User: shenwei1376

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Posts by shenwei1376

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Comment: A: Ballgown finds few DE genes compared to DESeq
... Hi, I am wondering if you have solved this issue. I am getting the same problem that ballgown gave significant less DF genes compared to DESeq2. It might not be the "FPKM" as my tophat-cufflink-cuffdiff produces the similar result as DESeq2. Thank you!@ ...
written 9 months ago by shenwei13760
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Comment: A: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Question, some error code like: "java development kit is needed" pumped up when I was running the run_pathfindR. Wondering how can I fix this? I already installed java on my Mac before! ...
written 12 months ago by shenwei13760
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Comment: C: reasons for htseq-count with zero features
... Thank you for your suggestions!! The library has been mapped to two indexed genomes. One is indexed based on a gtf file that is re-structured, so all the genes are re-grouped into transcripts (protein informs). Another one is indexed based on regular gtf file. The strange thing is all libraries work ...
written 13 months ago by shenwei13760
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reasons for htseq-count with zero features
... Hi everyone, I have asked this before, but want specify more this time. I have been using STAR-Htseq analyze the RNASeq data. Everything was find until recently, one of the library gives me 0 counts after the htseq-count. All the other libraries are fine, which means the gtf file or pipeline is fi ...
htseq-count rna-seq written 13 months ago by shenwei13760 • updated 13 months ago by genomax69k
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(Closed) htseq-count with zero features
... Hi everyone, I have recently got into an issue! I have been using htseq-count for RNASeq analysis. I was trying one indexed genome along with gtf file for the counting, it was all fine except the gtf file is grouped based on transcripts. As such, I indexed two new genomes (one from ensembl, anothe ...
htseq-count rna-seq written 13 months ago by shenwei13760
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Comment: C: calculating the fpkm from htseq counts
... Really thanks a lot!!! I think I already did the counts(dds, normalized=TRUE) during the differentiate expression analysis, but does deseq2 just normalize to the total reading number of the library? ...
written 13 months ago by shenwei13760
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Comment: C: calculating the fpkm from htseq counts
... I am a beginner of RNASeq. I already got the differentially expressed gene list from deseq2. Now, I am trying to get the expression value of all the genes, so I can do some other analysis just for the control. FPKM is the only the value I know to do this. I am not sure if there is other values I can ...
written 13 months ago by shenwei13760
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calculating the fpkm from htseq counts
... Hi everyone, I am trying to calculating the fpkm values from the htseq-count result. I think I already get the gene.size values for each of the transcript, while the "dds" contains more rows than the gene.size since there are NR##### (non-coding RNAs) in the dds list. When I was tryin tying to u ...
htseq R fpkm rna-seq written 13 months ago by shenwei13760 • updated 13 months ago by Charles Warden7.0k
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... Thank you so much for sharing the code! I am a beginner, just wondering if you could help with how to input the length information into the dds data. Many thanks! ...
written 13 months ago by shenwei13760
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low expression gene in RNASeq
... How everyone, I have recently got a RNASeq data. The mRNA level of my target gene is extremely low though the phenotype is very strong. All the change trend is consistent with qRT-PCR test, indicating the analysis pipeline should be fine. The knockdown is achieved through introducing shRNA and no ...
rnaseq low expression written 13 months ago by shenwei13760 • updated 12 months ago by Biostar ♦♦ 20

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