User: Smandape

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Smandape60
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6 days, 22 hours ago
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Posts by Smandape

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Identifying UMIs from fastq files
... For future reference, if OP here means Unique Molecular Indices (UMIs) and sample barcodes then it can mean different things. UMIs are also called molecular barcodes those serve different purpose than sample barcodes. Sample barcodes are used for demultiplexing where as molecular barcodes are used t ...
written 25 days ago by Smandape60
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Answer: A: How to integrate GSEA (genes) and MSEA (metabolites) analysis ?
... One way I am doing it is by using pathways those represent metabolites and genes in them. This way I am using the same pathways as background for running enrichment analysis. Although, for doing this I had to write my own enrichment analysis script. I didn't find any tool that will do what I want. ...
written 8 months ago by Smandape60
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BLAST RNASeq assembled fastq file to a gene sequence
... Hello Experts, I have de novo assembled RNASeq data. I want to see if my gene of interest shows up in this assembled data. The assembled RNASeq data is about 50GB. Would BLAST2BLAST / CLC genomics be a good option to find matching sequence in RNASeq data? What would be a good way to find my ge ...
gene rna-seq blast written 15 months ago by Smandape60
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Answer: A: How to link TCGA/GDC HTSeq or FPKM data with clinical data?
... There is a similar thread, [here][1], that mentions how to map UUIDs to TCGA barcode might answer your question. [1]: https://www.biostars.org/p/215175/ ...
written 2.5 years ago by Smandape60
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Answer: A: How to download Protein Expression data through manifest file from TCGA ?
... Maybe this is too late to reply but might help someone else as well. All the TCGA's data is available via Genomic Data Commons (GDC) portal. For downloading files using a manifest file you can use their Data Transfer Tool ([here][1]). It is easy to use and their documentation mentions in detail how ...
written 2.5 years ago by Smandape60
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Comment: C: Clutering Using Mcl Algorithm
... Can you open this file in notepad++? ...
written 5.9 years ago by Smandape60
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What Next After Contigs?
... I have contigs from a bacterial genome sequence. I am trying to find what would be the reference for this strain or where does it belong to in the phylogenetic tree. Also, what would be a good way to stitch them together? I did BLAST with individual contigs and also with all contigs together but I a ...
phylogeny assembly phylogenetics contigs written 5.9 years ago by Smandape60 • updated 5.9 years ago by sentausa640
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Comment: C: Convert Pmids To Nihmsid And Pmcid Using Eutils
... @Neilfws: Thank you so much for this direction. I didn't know how to move forward with my question. I also tried to put this question in Stackoverflow with possibility of webscraping but, no one replied and I was clueless how to do it with scrappy and other libraries in python. I was trying to get t ...
written 5.9 years ago by Smandape60
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Convert Pmids To Nihmsid And Pmcid Using Eutils
... I would like to know if I can convert PMID to NIHMSID, if there is no PMCID associated with that PMID and retrieve both of them if PMCID exists. I want to do this programmatically may be using eutils if possible. I know about this link http://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ that will do the work ...
webservice eutils written 5.9 years ago by Smandape60 • updated 5.9 years ago by Neilfws48k
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Comment: C: Finding Genome Coverage Using Random Reads
... Thank you. Well, I got the same answer but I was not sure if its correct. ...
written 7.7 years ago by Smandape60

Latest awards to Smandape

Supporter 2.2 years ago, voted at least 25 times.
Popular Question 4.2 years ago, created a question with more than 1,000 views. For What Next After Contigs?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How To Randomly Select 2 Sequences From Fasta Format In Perl?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Local Copy Of Pubmed
Popular Question 5.9 years ago, created a question with more than 1,000 views. For How To Randomly Select 2 Sequences From Fasta Format In Perl?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Convert Pmids To Nihmsid And Pmcid Using Eutils
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Local Copy Of Pubmed
Student 5.9 years ago, asked a question with at least 3 up-votes. For Local Copy Of Pubmed

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