User: kashiff007

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kashiff007130
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Posts by kashiff007

<prev • 49 results • page 1 of 5 • next >
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Bismark methylation for non-uniquely mapping BS-seq reads
... I am looking for the DNA methylation, specifically inside small RNAs; piRNA. I am mapping BS-seq reads on the genome with bismark. From the user guide of [bismark][1], it maps reads uniquely on the genome, which mean it reports first read with best score and discard rest of the alignment and if a re ...
dna methylation bismark small rnas sequencing written 16 days ago by kashiff007130
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Comment: C: Extract last exon annotation from each mRNA
... This works very fine just with change of database name from db.children to G.children. Thanks ...
written 3 months ago by kashiff007130
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Comment: C: Extract last exon annotation from each mRNA
... Here is sample of GFF I am using Kevin. Chr1 TAIR10 chromosome 1 30427671 . . . ID=Chr1;Name=Chr1 Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1 Chr1 TAI ...
written 3 months ago by kashiff007130
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Comment: C: Extract last exon annotation from each mRNA
... Hi liorglic, thanks for suggesting me this tool. I have tried and able to print the length of all exons from all genes, as I mentined in my previous [post][1] that I need only first and last 3 exons' and introns' length information. Here is my code: import GFFutils G = GFFutils.GFFDB ...
written 3 months ago by kashiff007130
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Extract last exon annotation from each mRNA
... I am working with GFF file, and found GFFutils is great tools to extract information from it. Although going through manual I am unable to extract the last exon's coordination from each mRNA. ...
gffutils written 3 months ago by kashiff007130
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Average length of each exon and intron
... Hi, I want to estimate the average length of each exon and intron (first 3 and last 3) from the gff/gtf file, something shown below: exon1 500 exon2 400 exon3 300 exon-3 450 exon-2 300 exon-1 299 intron1 500 intron2 400 intro ...
gtf bed gff next-gen bedtools written 3 months ago by kashiff007130
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Comment: C: Interpreting Bismark Methylation Extractor output
... Use **bedGraph2cytosine** to associate your coverage file with context: bedGraph2cytosine -o --genome_folder -CX ...
written 5 months ago by kashiff007130
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Comment: C: Plot read density across a normalized gene model for its each exon/intron length
... Thanks but unfortunately none of the above work for gene model normalization. ...
written 7 months ago by kashiff007130
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Comment: C: Plot read density across a normalized gene model for its each exon/intron length
... https://advances.sciencemag.org/content/advances/4/8/eaat2142.full.pdf ...
written 7 months ago by kashiff007130
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Plot read density across a normalized gene model for its each exon/intron length
... I know there are several tool which can plot ChIP-seq score based on annotation file (GTF/GFF3/BED), but Is there any standard tools in R/python which can plot and normalize to gene model for its each exon/intron length? I am looking for the following output: ![enter image description here][1] He ...
deeptools next-gen chip-seq R python written 7 months ago by kashiff007130 • updated 7 months ago by benformatics1.6k

Latest awards to kashiff007

Popular Question 2 days ago, created a question with more than 1,000 views. For How to generate pair-wise alignments for all the orthologous gene pairs at once?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to generate pair-wise alignments for all the orthologous gene pairs at once?
Supporter 6 months ago, voted at least 25 times.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: plot error x y length difference
Scholar 11 months ago, created an answer that has been accepted. For A: Combining two columns in a tab-delimited file where there is a zero in one
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to generate pair-wise alignments for all the orthologous gene pairs at once?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Cufflinks generating multi-transcripts
Scholar 2.8 years ago, created an answer that has been accepted. For A: Combining two columns in a tab-delimited file where there is a zero in one

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