User: kashiff007

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kashiff00750
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5 days, 22 hours ago
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Posts by kashiff007

<prev • 29 results • page 1 of 3 • next >
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Merge MNase-seq bam files from replicates.
... I am working with MNase-seq data. I have few replicates from samples. For the analysis, I have to work on distogram (histograms of distances between mapped reads’ start positions aligning in opposing orientation), phasogram (histograms of distances between mapped reads’ start positions aligning in t ...
replicates mnase-seq merge next-gen bam-files written 5 days ago by kashiff00750
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Answer: A: How to distinguish if a gene is a paralogue or an isoform?
... According to the basic definition isoforms are coming from same gene, so their location should be same in the genome. At least, in most cases TSS and TTS are usually same for all transcript. While paralogs are the result of duplication so their position differ from the original gene. Technically par ...
written 5 weeks ago by kashiff00750
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Comment: C: Number of discovered genes in genome does not correspond with published annotati
... Yes, you are right. Since your question mainly concerned about number of "discovered genes" in annotation file, it will for sure give the total count of genes (which may have more that one CDS for sure). Also, I have not mentioned in my previous comment that it will provide the total number of CDS f ...
written 5 weeks ago by kashiff00750
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Comment: C: Number of discovered genes in genome does not correspond with published annotati
... It extract 3 column of gff file (which has information like gene, intron, exon, miRNA etc) and then count the number of occurrence in whole gff file. In other words, you will get the total number of genes in your gff file. ...
written 5 weeks ago by kashiff00750
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Comment: A: Number of discovered genes in genome does not correspond with published annotati
... **Full information of your GFF file** awk '{print$3}' | sort | uniq -c your.gff ...
written 5 weeks ago by kashiff00750
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Answer: A: Convert Fasta format to MEME-motif format
... **Full FIMO Pipeline Step** fasta-get-markov sequences.fasta > sequences.bg mkdir temp fasta-grep '.+' -dna -o < motif_sites.fasta > temp/motif_name.txt sites2meme -bg sequences.bg temp > motif_name.meme fimo --bgfile sequences.bg motif_name.meme Genome_to_be_search ...
written 5 weeks ago by kashiff00750
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Answer: A: Is There Is Tool For Variable Tandem Repeats Finding?
... See also, MEME-suite ([http://meme-suite.org/doc/meme-format.html][1]). It's different tools by which you can discover new repeats (MEME), can look for repeat/motif enrichment in particular region of the genome (CentrMo), can scan your repeat/motif in the genome (FIMO) and many more related analysis ...
written 5 weeks ago by kashiff00750
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Comment: C: How to subset S4 list with 5 Granges elements
... It's the problem of R dataframe and file handling. Please tag R, data.frame and related tags. Also, please provide the file sample from which you want to extract the data. Without knowing S4 list structure it's hard to imagine the solution. ...
written 5 weeks ago by kashiff00750
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Comment: C: Multiple sequence alignment and visualisation for bacterial genomes
... This is too complex. To make it simple, I will start with selecting gene region (annotated sequences) of a reference genome (Lets say *E. coli* in your case). This will lead to find all the orthologs in different bacterial species: use MCScanX ([http://chibba.pgml.uga.edu/mcscan2/][1]) for this purp ...
written 5 weeks ago by kashiff00750
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Answer: A: Convert Fasta format to MEME-motif format
... Follow these steps: - Generate background files by: fasta-get-markov - Use iupac2meme to generate MEME motif file ...
written 5 weeks ago by kashiff00750

Latest awards to kashiff007

Popular Question 9 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?
Popular Question 9 months ago, created a question with more than 1,000 views. For Cufflinks generating multi-transcripts
Scholar 18 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

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