User: sunil.mangalam

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New User
Location:
United States
Last seen:
2 years ago
Joined:
3 years, 11 months ago
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Posts by sunil.mangalam

<prev • 6 results • page 1 of 1 • next >
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Transcript to gene mapping of overlapping transcripts from cuffcompare
... Hi Forum, We did RABT assembly of mouse transcriptome using cufflinks and stringtie. Cuffcompare produced many genes of the class code O. While mapping these transcripts to gene level, cuffcompare grouped transcripts of class code o to the parent gene. But many o transcripts look very different from ...
de novo assembly rna-seq classcode 0 written 2.0 years ago by sunil.mangalam10 • updated 22 months ago by Biostar ♦♦ 20
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Cufflinks genome guided de novo transcript assembly- increase in ambiguous reads
... Hi forum, I am doing denovo transcript assembly using cufflinks.In parellel, I am using featurecounts to count against Gencode M7. My data is 100bpPE and unstranded mouse RNASeq. Our workflows are: STAR-Featurecounts (against Gencode M7) or STAR-Cufflinks Denovo transcript assembly-cuffmerge - Featu ...
rna-seq denovo assembly written 3.6 years ago by sunil.mangalam10 • updated 3.6 years ago by andrew.j.skelton735.7k
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Denovo transcriptome assembly
... Hi Forum, We have some RNA-Seq data generated using Nugen's Ovation RNA-Seq System V2 kit.I plan to do denovo transcript assembly using cufflinks with this data. But when I look at the BAM files, I see many genes which have quite a lot of reads in introns. My feeling is that most of it comes from pr ...
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DeSeq2 data transformation for visualization
... Hi,  I am facing some difficulties with data transformations of my single cell RNA-Seq data analyzed using DESeq2. This data set is different from typical RNA-Seq experiments.. For example, there is a subset of genes which will be present in one group and totally absent in the other, unlike typical ...
deseq2 data transformation written 3.7 years ago by sunil.mangalam10 • updated 3.5 years ago by Biostar ♦♦ 20
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Answer: A: Cufflinks Crashes Because Of Mitochondrial Rna Abundance
... Hi, We recently had a similar experience with cufflinks running out of memory and crashing. Our library also has mitochondrial RNA reads. Can you please share what error you had? ...
written 3.9 years ago by sunil.mangalam10
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Cufflinks denovo mapping runs out of memory
... Hi all, We have some questions about cufflinks denovo assembly which we are grappling with. We could not do denovo assembly on our data because cufflinks ran out of memory we used 600gb per sample, the maximum in our cluster). But we could get an assembly from one of our samples which had a much low ...
software error rna-seq written 3.9 years ago by sunil.mangalam10

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