User: rajeev.vikram

gravatar for rajeev.vikram
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30
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New User
Location:
Taiwan
Last seen:
2 years, 1 month ago
Joined:
4 years, 9 months ago
Email:
r************@gmail.com

Posts by rajeev.vikram

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Downstream analysis of bam files from scRNA-Seq Data
... Thanks Ryan, This makes things a lot more clear. ...
written 2.2 years ago by rajeev.vikram30
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Downstream analysis of bam files from scRNA-Seq Data
... Hi, I am new to single cell RNA-Seq, and am trying to find a workflow related question. I have aligned about 1500 cells from two different experiments (but using same experimental procedure). I am wondering how do I go ahead with differential expression analysis. Should I merge all the bam files ...
single cell rna-seq next-gen rna-seq written 2.2 years ago by rajeev.vikram30 • updated 2.2 years ago by Devon Ryan95k
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Comment: C: Questions about Alignment and downstream workflow for scRNA-Seq Data
... I was talking from a bulk-seq perspective, where we have one(or two) fastq files per sample. I am not really aware of how scRNA-Seq works, probably in batches, but how, thats why I asked the question. An example would be great. ...
written 2.3 years ago by rajeev.vikram30
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Comment: C: How to fix 5'UTR annotation with RNA-seq data?
... It seems that you want to generate a consensus transcriptome for your samples, you can use the StringTie transcript assembler for the purpose. specifically, the option: StringTie --merge to generate a merged (consensus) gtf file from your samples. It will also generate the consensus isoforms. You sh ...
written 2.3 years ago by rajeev.vikram30
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Answer: A: How to fix 5'UTR annotation with RNA-seq data?
... Hello, how many samples are you using? are all of them consistently showing hits to the same region of the annotated transcript (UTR)? Did you verify the reported isoforms with your alignment hits? There is "No" way to change the pattern of reported hits of an alignments. You can include/exclude so ...
written 2.3 years ago by rajeev.vikram30
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Questions about Alignment and downstream workflow for scRNA-Seq Data
... Hi, I am new to single cell (SC) RNA-Seq and have a rather naive q regarding the alignment of single cell fast q files. As, there are hundreds/thousands of fast q files corresponding to their respective SCs, How do we align all these fastq files in parallel? should one align a few fastq files at ...
single cell rna-seq rna-seq written 2.3 years ago by rajeev.vikram30 • updated 2.3 years ago by Devon Ryan95k
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Answer: A: total newbie staring into headlights
... Considering you have =0 NGS/RNA Seq experiment Step 1 - Learn about Bioinformatics and basic alignment techniques Time = 15-30 days Step 2 - Learn the basics of Unix, Python, Perl and R these are absolute essentials (But Just the basics). Time - 3-6 months A good book to refer : ...
written 3.7 years ago by rajeev.vikram30
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Answer: A: A Basic question regarding lncRNA identification pipeline.
... Thanks, but my question is slightly different, , basically, after top-hat assembly with bowtie2 , I Used RABT assembly in cufflinks and then merged all transcripts (elegant= gtf file of annotated transcripts), then did cuffmerge of the replicates. After running cuffcompare with r- given as annotated ...
written 4.0 years ago by rajeev.vikram30
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A Basic question regarding lncRNA identification pipeline.
... Hi, I have been analyzing RNA-Seq data sets of some Breast cancer cell lines to create a high confidence list of expressed lncRNAs. However as, I am new to NGS, I cannot figure out how do I filter out the known Expressed gene/protein coding transcripts from my annotation file after cufflinks assemb ...
pipeline rna-seq lncrna written 4.0 years ago by rajeev.vikram30

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