User: Manvendra Singh
Manvendra Singh • 2.1k
- Reputation:
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- Berlin, Germany
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- manvendr7
- Last seen:
- 9 months ago
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- Email:
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PhD Student (Mobile DNA Group) at Max-Delbruck Centre fur Molecular Medicine
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... Hi Dear,
I would recommend not to filter anything.
Dataset: homo sapiens genes Attributes: Ensembl gene ID. Ensembl transcript ID.
first get the data in tsv, and then just remove the duplicates
hth ...
written 3.6 years ago by
Manvendra Singh • 2.1k
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... [these literatures should help you
[Brain transcriptome][1]
[The populations sampled span the geographic breadth of human migration history; EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP)][2]
[1]: http://www.pnas.org/content/112/2 ...
written 3.6 years ago by
Manvendra Singh • 2.1k
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... Dude, you are confused. May be first you get your question right.
Protein is made by reading mRNA in the 5' to 3' direction and making new protein from its amino end (N-terminus) towards its carboxyl end (C-terminus).
so In your case, 1st amino acid would have N terminal and 149th would have C-term ...
written 3.6 years ago by
Manvendra Singh • 2.1k
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... Differential Isoform expression is consequence of Alternate splicing
If the overall expression of gene is not changing but isoform expression is differential then its the case isoform switch in your case.
you can perform gene set enrichment analysis to see if alternatively spliced transcripts are p ...
written 3.7 years ago by
Manvendra Singh • 2.1k
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... Did you try running Cufflinks2 RABT assembly; I would suggest you to run in both mode; default and RABT and see if you can catch your desired isoform ...
written 3.8 years ago by
Manvendra Singh • 2.1k
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... Its just mean of all transcripts to assign one value to gene
PS: Its quite old post, now this job is done by featureCount where we calculate counts on gene_id but not on transcript_id given in gtf files ...
written 3.8 years ago by
Manvendra Singh • 2.1k
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... May be assign, mean of all probes to its target gene.
then choose only those genes that are detectable in all platforms.
once you have equal number of rows in different datasets, you can easily merge it by "merge" function in R ...
written 3.8 years ago by
Manvendra Singh • 2.1k
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Answer:
A: Time series microarray data
... Canser ?
If you mean Cancer progression timed series data, you can look into TCGA datasets
Tier4 has normalized expression data
https://tcga-data.nci.nih.gov/docs/publications/tcga/? ...
written 3.8 years ago by
Manvendra Singh • 2.1k
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... Yes, I have seen some papers where upregulated and downregulated genes are categorized separately on GO term;
Once you get significant level of GO term in the subset of genes, you can go for pathway or network analysis to see the enrichment of your detected genes in certain pathway or process
...
written 4.8 years ago by
Manvendra Singh • 2.1k
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... Hi All,
I was mapping paired end fastq files by tophat2 on 10 threads, it got stucked during Searching for junctions via segment mapping. Everything seems to be alright; Here is the output
[2015-08-19 00:16:41] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2015-08- ...
written 4.8 years ago by
Manvendra Singh • 2.1k
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