User: Renesh
Renesh • 1.9k
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Posts by Renesh
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... 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
Renesh • 1.9k
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... File compression options (--gzip or --bzip2) are not available in fasterq-dump ...
written 8 weeks ago by
Renesh • 1.9k
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... 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
Renesh • 1.9k
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... 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
Renesh • 1.9k
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... 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
Renesh • 1.9k
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3
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659
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... 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
Renesh • 1.9k
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... 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
Renesh • 1.9k
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3
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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
Renesh • 1.9k
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... Can you please provide the one or few sequences containing "TT[TA]TTGC..CCCACTG"? ...
written 5 months ago by
Renesh • 1.9k
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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
Renesh • 1.9k
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