User: Renesh

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Renesh1.9k
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Posts by Renesh

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Answer: A: Creating a fasta filter by gene length
... Simplly use `len(seq_record) < sys.argv[2]` or `len(seq_record.seq) < sys.argv[2]` Alternatively, you can try `bioinfokit` in Python from bioinfokit.analys import fasta fasta_iter = fasta.fasta_reader(file='fasta_file') for record in fasta_iter: header, sequence = re ...
written 8 weeks ago by Renesh1.9k
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Comment: C: What would be the equivalent fasterq-dump options?
... File compression options (--gzip or --bzip2) are not available in fasterq-dump ...
written 8 weeks ago by Renesh1.9k
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Answer: A: Does alternative splicing analysis not so prevalent in plant study?
... Yes, the alternative splicing (AS) rate is very higher in humans (~95%) as compared to plants (~60%). The seemingly lower number of genes undergoing AS in plants when compared to humans (~95%) could be due to lack of enough studies or in-depth annotations of the plant genomes. In early reports dati ...
written 9 weeks ago by Renesh1.9k
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Answer: A: Using ComBat-seq on transcript counts
... ComBat-Seq takes input as raw un-normalized data as input and addresses the batch effects using a negative binomial regression model. You can use featureCounts (https://academic.oup.com/bioinformatics/article/30/7/923/232889) or htseq-count (https://htseq.readthedocs.io/en/release_0.11.1/count.html) ...
written 9 weeks ago by Renesh1.9k
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Comment: C: How to do unsupervised clustering of RNA-Seq data
... You can try PCA https://reneshbedre.github.io/blog/pca_3d.html and heatmap with hierarchical clustering https://reneshbedre.github.io/blog/hmap.html ...
written 9 weeks ago by Renesh1.9k
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Answer: A: Extract sequences from a list of ID
... You can also try Python package `bioinfokit` (v1.0.2 or later) for extracting the sequences from the FASTA file (check how to install https://reneshbedre.github.io/blog/howtoinstall.html#how-to-install) `from bioinfokit.analys import fasta` `fasta.extract_seq(file='Trinity.fasta', id='id.txt')` C ...
written 11 weeks ago by Renesh1.9k
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Comment: C: EdgeR analysis with CPM normalzed counts
... Hi, If you have CPM normalized counts from edgeR, then it should be already normalized for library size. You do not need to again calculate `calcNormFactors` you can see here https://reneshbedre.github.io/blog/expression_units.html#tmm-trimmed-mean-of-m-values ...
written 3 months ago by Renesh1.9k
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Comment: C: Plant orthologous genes
... You can have the orthologous genes in Arabidopsis for all rice genes at Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html#) The best way is to do the reciprocal BLAST analysis of the transcript sequences and retain the best hits from two species to identify the orthologous genes. ...
written 4 months ago by Renesh1.9k
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Comment: C: Python: regular expression searching error
... Can you please provide the one or few sequences containing "TT[TA]TTGC..CCCACTG"? ...
written 5 months ago by Renesh1.9k
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Answer: A: Heatmap for gene expression
... Hi akashagri19, Thank you for using the bioinfokit for heatmap. You need to first import your data as a pandas dataframe. You can not use `get_data` as it is for internal example datasets. Import your dataset as import pandas as pd df = pd.read_csv('your_data.csv') # for CSV file df ...
written 5 months ago by Renesh1.9k

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