User: gayachit

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gayachit150
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Posts by gayachit

<prev • 37 results • page 1 of 4 • next >
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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 1 day ago by gayachit150
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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 1 day ago by gayachit150
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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 2 days ago by gayachit150
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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 2 days ago by gayachit150
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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 2 days ago by gayachit150
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Comment: C: Biopython Pairwise Alignment output
... Is this similar to what you need? https://www.biostars.org/p/237209/ ...
written 3 days ago by gayachit150
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Comment: C: RNA de novo assembly - blasts - KEGG - GO
... What does singleton of assembly mean? I don't exactly know how to do that because by definition singletons mean the reads having no pair. But here's an idea, you identify the singleton reads, map the reads on the assembly using bowtie2 or similar alignment tool and identify where the singleton reads ...
written 6 days ago by gayachit150
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Comment: C: RNA de novo assembly - blasts - KEGG - GO
... No not trinity fasta. You do a trimmomatic before you assemble. This is a pre-processing step for raw reads where you can remove adaptors and low quality sequences. Here's the manual which has the command as well http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32 ...
written 7 days ago by gayachit150
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Comment: C: RNA de novo assembly - blasts - KEGG - GO
... Yes. And sorry about the singletons, inchworm in trinity actually does not include kmer singletons in the initial contig step. You can get the number by running trimmomatic for raw reads. Singletons are nothing but the reads which don't have a corresponding pair. It generates left and right files f ...
written 7 days ago by gayachit150
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Comment: C: RNA de novo assembly - blasts - KEGG - GO
... The cdhit-est command that you gave is fine. It should have generated a cluster file as given in the manual for cdhit. You can count the clusters from that. I think it also generates a stats file. Atleast the online version does. ...
written 8 days ago by gayachit150

Latest awards to gayachit

Scholar 22 hours ago, created an answer that has been accepted. For A: How to get the phastcons score for protein coding genes and lncRNAs?
Scholar 10 days ago, created an answer that has been accepted. For A: How to get the phastcons score for protein coding genes and lncRNAs?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to run Genscan on large files
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Do we need to estimate effective transcriptome size before sequencing?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Need Help with RNA secondary structure folding

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