User: ashish

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ashish250
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Posts by ashish

<prev • 109 results • page 1 of 11 • next >
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Comment: C: Help with genome guided de novo assembly in trinity
... Why do you want to do a denovo assembly of you RNA-seq reads which come from zebrafish which already has a well annotated genome as h.mon pointed out. Denovo transcriptome assembly is done for organisms whose genome information is not available. ...
written 1 day ago by ashish250
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Comment: C: about the batch effects
... Did you first check if there are any batch effects in the 3 situations? ...
written 2 days ago by ashish250
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Answer: A: Any recommendation for pathway analysis of Wheat RNA-seq data?
... You can use [plant reactome][1] for wheat pathway mapping. The website is currently down for maintenance till 8th december. [1]: https://plantreactome.gramene.org ...
written 7 days ago by ashish250
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Comment: C: Well studied gene networks/pathways in rice
... Its actually not clear what kind of networks you are talking about. If its co-expression networks than [this][1] is a good resource where they have used RNA-seq data. There is [another][2] good resource but it is based on microarray data. [1]: http://expression.ic4r.org/index [2]: http://ric ...
written 8 days ago by ashish250
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Comment: C: finding orthologs in A. thaliana, using odd protein identifier
... I think you will have to retrieve all sequence if you want GO terms for all of them. After getting the GO terms you can apply a cutoff based on the significance test to filter enriched significant terms. If you have any other data such as expression or interaction data, you can choose sequences of ...
written 18 days ago by ashish250
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Comment: C: finding orthologs in A. thaliana, using odd protein identifier
... You need to retrieve the sequences and then use them as input in GO tools. To find orthologs in arabidopsis just do a blast search and keep the top hits as orthologs. You can try [agriGO][1] to get GO terms using corresponding Arabidopsis IDs. agriGO has an option to map sequences from non-model pla ...
written 19 days ago by ashish250
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Comment: C: How To Blast A Sequence Against Multiple Databases
... If you have limited RAM (4Gb) then sometimes it is not possible to concatenate all the chromosome fasta files and then create the database at once. I just tried this on a 4GB RAM laptop with wheat genome (17Gb) and it stalled the laptop. Creating databases for individual chromosomes and then combini ...
written 23 days ago by ashish250
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Comment: C: Extract Transcript sequence from fastq file (Plant RNA-Seq data)
... [MAKER-P][1] is good. [1]: http://www.yandell-lab.org/software/maker-p.html ...
written 4 weeks ago by ashish250
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Comment: C: Extract Transcript sequence from fastq file (Plant RNA-Seq data)
... You can extract transcript sequences directly from [ensembl plants biomart][1], you don't need RNA-seq data for that. In case it is transgenic with fused transcripts or something like that, then you can use blast to extract reads from fastq file and then assemble them. [1]: https://plants.ense ...
written 4 weeks ago by ashish250
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Comment: C: edgeR dispersion value (common BCV (square- root-dispersion)) when no replicates
... I have done the same thing on wheat once. I tried multiple approaches but without replicates it is not very useful. The best results I found which matched wet lab data were from GFOLD. Here also you will not get any statistics, just ranked genes. You can use the top and below 200/300/400 genes. Thi ...
written 12 weeks ago by ashish250

Latest awards to ashish

Great Question 11 days ago, created a question with more than 5,000 views. For levels in gene ontology
Centurion 4 weeks ago, created 100 posts.
Voter 11 weeks ago, voted more than 100 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 10 months ago, created a question with more than 1,000 views. For Gap treatment in MEGA for ML phylogeny
Popular Question 10 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 10 months ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 14 months ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 14 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 14 months ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 15 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 17 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 19 months ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 21 months ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 22 months ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 24 months ago, created a question with more than 1,000 views. For heatmap using FPKM values
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Scholar 2.9 years ago, created an answer that has been accepted. For A: please help me retrieve these sequences

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