User: Vishaka Datta

gravatar for Vishaka Datta
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India
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4 years, 1 month ago
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4 years, 9 months ago
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Posts by Vishaka Datta

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Comment: C: Best Practices For Using Fimo For Motif Scanning
... Ah, now I see what you mean. Thanks :) ...
written 4.5 years ago by Vishaka Datta80
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Comment: C: Help in cufflinks -- all the FPKM values are 0
... The command you've used looks quite complicated. Are you sure the correct genome annotation file is being passed to cufflinks? Check the value of all the shell variables used to see if it's the correct file being opened. ...
written 4.5 years ago by Vishaka Datta80
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Answer: A: use bedtools to find overlaps of bed and gff files
... You can find intergenic regions of your GFF file by using complementBed. You require a fasta index file as an input to this method though (usually a file with a .fai extension). The fasta index file can be created by using the faidx tool from SAMtools. Here's an example pipeline for finding overlaps ...
written 4.5 years ago by Vishaka Datta80
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Comment: C: Best Practices For Using Fimo For Motif Scanning
... But wouldn't the sequence file contain subsequences that match the motif you are searching for? This would result in background frequencies estimates that are skewed towards sequences containing motifs, which would increase the false discovery rate of motif searches. I didn't quite follow what is w ...
written 4.6 years ago by Vishaka Datta80
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Comment: C: Difference between TFBS Perl/Biopython motif search and FIMO
... FIMO is part of the MEME suite, and it does the job of finding significant matches to a motif. MAST is similar to FIMO in some respects, but does more sophisticated stuff, I have been trying to replicate results from a paper that used the TFBS Perl module for finding motif matches. They found a muc ...
written 4.6 years ago by Vishaka Datta80
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Answer: A: Problems aboout Cufflinks results
... I'm fairly new to Cufflinks myself. From what I've seen, a newly discovered transcript or exon ends up being tagged as CUFF.* In the example given by you : chr1    Cufflinks    exon    134773    139696    1000    -    .    gene_id "CUFF.31"; transcript_id "NR_039983"; exon_number "1"; FPKM "0.7545 ...
written 4.6 years ago by Vishaka Datta80
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Difference between TFBS Perl/Biopython motif search and FIMO
... I've learnt a motif file for a TF from running meme on a ChIP-seq data set. I now want to search for matches to this motif in the remainder of my ChIP-seq data set. One option is to use FIMO with the motif file to search for motif occurrences, and the other is to use the biopython motif search pack ...
fimo chip-seq biopython motif search written 4.6 years ago by Vishaka Datta80
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Comment: C: How is FPKM variability handled?
... There are comparisons between FPKM and counts with respect to which measures and methods of modelling RNA-seq data tend to give better differential expression results.  ...
written 4.8 years ago by Vishaka Datta80
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Comment: C: How is FPKM variability handled?
... Reasons for errors - Off the top of my head : 1) Sequence reads might align to multiple locations within the genome. This makes assigning a given read to a particular gene ambiguous. Cufflinks has a few ways of dealing with it (the multi-read correct option, for instance). See the cufflinks manual ...
written 4.8 years ago by Vishaka Datta80
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Answer: A: How is FPKM variability handled?
... How much can one trust them : The cufflinks output files (genes.fpkm_tracking, isoforms.fpkm_tracking) will contain confidence intervals for each of the FPKM estimates (under the headings FPKM_conf_lo and FPKM_conf_hi). Similarly, cuffdiff output also contains the FPKM estimates and confidence inter ...
written 4.8 years ago by Vishaka Datta80

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Scholar 4.8 years ago, created an answer that has been accepted. For A: How is FPKM variability handled?

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