User: gayachit

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gayachit200
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Posts by gayachit

<prev • 51 results • page 2 of 6 • next >
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Answer: A: Pathway targeted genes
... If by targets you mean for further qPCR or such analysis then yes. You can confirm by doing classification using DAVID (https://david.ncifcrf.gov/). Take the list of significant DE genes and classify and check the NFKB pathway. ...
written 5 months ago by gayachit200
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Answer: A: Sort header from the multifasta sequnce file into only gene name
... Very rough solution but should work: sed -e 's/.*GN=/>/' -e 's/PE=.*//g' your_file.txt > new_file.txt ...
written 5 months ago by gayachit200
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Answer: A: What does "passes" in MIRA mean?
... Passes defines how many iterations of the whole assembly process are done. Default is 0. Default 0 lets MIRA choose automatically the number of passes and the kmer sizes used in each pass ...
written 5 months ago by gayachit200
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Comment: C: splitting test and train data
... Yes, you can split your train and test data with sklearn. https://machinelearningmastery.com/evaluate-performance-machine-learning-algorithms-python-using-resampling/ You can check the above site for many other examples with code ...
written 5 months ago by gayachit200
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Comment: C: Ways to convert fasta to faa file for functional annotation?
... Is there a reason you want to convert? I think eggNOG mapper takes CDS sequences also as input. ...
written 6 months ago by gayachit200
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Comment: C: Biopython Pairwise Alignment output
... For 1: https://www.megasoftware.net/mega1_manual/Phylogeny.html#5-1 under tree building methods For 2: MEGA is used by many for phylogenetic analysis and has been cited in multiple papers. There are a number of tools creating phylogenetic trees. You need to google about the methods they use. ...
written 6 months ago by gayachit200
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Comment: C: Biopython Pairwise Alignment output
... Sounds like you need a distance method like neighbor joining method. You could use MEGA tool: https://www.megasoftware.net/ It states in the manual that In distance methods, a pairwise evolutionary distance is computed for all species or OTUs to be studied, and a phylogenetic tree is constructed by ...
written 6 months ago by gayachit200
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Answer: A: the transcription fasta file of Caenorhabditis elegans
... I see the CDS file. Thats protein coding transcript file. Also the CDNA file ...
written 6 months ago by gayachit200
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Comment: C: Biopython Pairwise Alignment output
... Actually I am guessing from the assignment that what needs to be done is to do pairwise alignments of all the sequences, generate a distance matrix and from that get a guide tree to make a phylogeny. Atleast thats how the method goes. BTW i found this. Hope it helps a little. http://scikit-bio.or ...
written 6 months ago by gayachit200
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Comment: C: Biopython Pairwise Alignment output
... Is this similar to what you need? https://www.biostars.org/p/237209/ ...
written 6 months ago by gayachit200

Latest awards to gayachit

Scholar 5 months ago, created an answer that has been accepted. For A: How to get the phastcons score for protein coding genes and lncRNAs?
Scholar 6 months ago, created an answer that has been accepted. For A: How to get the phastcons score for protein coding genes and lncRNAs?
Scholar 6 months ago, created an answer that has been accepted. For A: How to get the phastcons score for protein coding genes and lncRNAs?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to run Genscan on large files
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Do we need to estimate effective transcriptome size before sequencing?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Need Help with RNA secondary structure folding

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