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User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania • 1.8k
Reputation:
1,840
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
21 hours ago
Joined:
5 years, 1 month ago
Email:
c**************@gmail.com

All answered queries can also be found on github https://github.com/cparsania/biostar_queries

 

 

Posts by Chirag Parsania

<prev • 218 results • page 1 of 22 • next >
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Comment: C: Get summary of aligned sequences
... Can you elaborate a little more on generating clusters? I mean how can I do that and with the clusters how to proceed with downstream phylogeny. ...
written 12 weeks ago by Chirag Parsania • 1.8k
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Comment: C: Get summary of aligned sequences
... Yes. I want to generate statistics out of that. For example, the distribution of gaps, number of conserved columns etc. ...
written 12 weeks ago by Chirag Parsania • 1.8k
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Get summary of aligned sequences
... Hi, I have aligned a set of ~3000 protein sequences. Next, I want to do is to generate a phylogenetic tree. Before that, I want to check the quality of the alignment. Is there any way to get a summary of aligned sequences quickly? Also, can anyone suggest a tool to process the aligned sequences be ...
fasta sequence alignment written 12 weeks ago by Chirag Parsania • 1.8k
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Comment: C: plot tss profile
... Try [EnrichHeatmap][1] [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/EnrichedHeatmap/inst/doc/EnrichedHeatmap.html ...
written 3 months ago by Chirag Parsania • 1.8k
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Tool: TidyWrappers : an R package to deal with an object tbl
... Dear Biostarians, As we all know that `tidyverse` has shifted the paradigm the way R was being used then and now. And therefore, it has become necessary to learn `tidyverse` to do efficient programming in R. For newcomers, it takes time to become familiar with tools given in `tidyverse` and to ap ...
gene-expression R chip-seq wrappers rna-seq tool written 3 months ago by Chirag Parsania • 1.8k
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Comment: C: Empty .fa file after fa_some_records
... I assume query (genelist.txt) should match exactly to the headers in multi-fasta (genoma.fna) file ...
written 3 months ago by Chirag Parsania • 1.8k
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Comment: C: Reading a tab separated file
... Try following. It woorked. library(magrittr) readr::read_delim("inputfile.txt" ,delim = "\"/t\"") %>% dplyr::select("choc","beer" ,"elec") # A tibble: 20 x 3 choc beer elec 1 1451 96.3 1497 2 2037 84.4 1463 3 2477 91.2 1648 ...
written 3 months ago by Chirag Parsania • 1.8k
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Comment: C: Removal of sequences that is partial of a longer sequences in multifasta file
... You can try program [CD-HIT][1] with Sequence Identity Parameter = 1. It will cluster all sequences which are identical and return you longest one for each cluster. [1]: http://weizhongli-lab.org/cdhit_suite/cgi-bin/index.cgi?cmd=cd-hit ...
written 3 months ago by Chirag Parsania • 1.8k
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Answer: A: Qcov Vs QcovHSP
... >Why does my query coverage exceed 66.66% for the 151bp sequences? I can see that it doesn't go above 80% but I still see alignments with 73-74% Qcov (higher than 66%) How is this possible? Well, you see all your queries are of length 100 at least in the data you posted. Also, you have Qcov more ...
written 3 months ago by Chirag Parsania • 1.8k
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Comment: C: FASTA file split
... try command faSplit given by [UCSC utilities][1]. [1]: http://hgdownload.soe.ucsc.edu/admin/exe/ ...
written 4 months ago by Chirag Parsania • 1.8k

Latest awards to Chirag Parsania

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Why cufflink gives two transcripts/isoforms for one particular ORF ??
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Why cufflink gives two transcripts/isoforms for one particular ORF ??
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Scholar 3 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 3 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Great Question 3 months ago, created a question with more than 5,000 views. For Extract reads from bam/sam files using read id
Popular Question 7 months ago, created a question with more than 1,000 views. For Why cufflink gives two transcripts/isoforms for one particular ORF ??
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Scholar 9 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How can I separate column names in to different columns to perform downstream an
Good Question 11 months ago, asked a question that was upvoted at least 5 times. For How to find intron co-ordinates from the gff file?
Scholar 12 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Epic Question 13 months ago, created a question with more than 10,000 views. For Z-Score calculation by heatmap.2
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 15 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 17 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Appreciated 17 months ago, created a post with more than 5 votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Scholar 17 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 18 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Appreciated 19 months ago, created a post with more than 5 votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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