User: a.rex

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a.rex150
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Posts by a.rex

<prev • 76 results • page 1 of 8 • next >
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Answer: A: Comparing genome assemblies of the same animal
... I have two protein fasta files of the same animal. One is an assembly with a small N50; the other pacbio one has a larger N50. I wish to blastp the bad genome against the better one; after performing this I want to extract out the query length and hit length. I will then blastp the better one agai ...
written 2 days ago by a.rex150
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Comment: C: Comparing genome assemblies of the same animal
... Yes, I suppose I can adjust the Snakefile? ...
written 3 days ago by a.rex150
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Comparing genome assemblies of the same animal
... I have a genome of a species, which I have annotated in house. The N50 for this genome is around 41,000. I have another, better genome, of the same species, which I have also annotated in house. The N50 for this is 4,000,000. I suspect my poorer genome has split and incomplete transcripts, whic ...
assembly written 3 days ago by a.rex150
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Comment: C: Perform GO analysis on genome
... Hello - apologies for that. It is a new genome for an obscure animal. I have annotated using mikado, and have produced a translated longest ORF file ...
written 4 days ago by a.rex150
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Perform GO analysis on genome
... I have a protein fasta file, for each longest ORF for an annotated locus in my genome. Could anyone advise how best to perform a GO analysis on the this file, such that for each locus I have a GO id? ...
go analysis written 4 days ago by a.rex150 • updated 4 days ago by seidel6.6k
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How do i extract rows from a bedfile that have a certain bedscore?
... I have a typical bedfile - I want to extract out rows that have a read coverage score/bedscore of >100. Any tips on how to do this would be much appreciated. ...
bed parse written 10 days ago by a.rex150 • updated 10 days ago by Alex Reynolds25k
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How do I perform a motif search on a specific fasta sequence?
... I have an annotated genome file, and I have a potential ncRNA that could be an eRNA. I have extracted this sequence to a fasta file, and want to use homer for scanning transcription factor binding sites (i.e. to work out whether it is a potential enhancer). How can I do this? I have tried with t ...
homer enhancer written 12 days ago by a.rex150 • updated 11 days ago by RamRS17k
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How to search for TF binding sites upstream of specific genes?
... I have a reference genome and set of annotations in a gff file (which of course I can easily convert to a fasta/bed etc). I have a list of candidate genes which I want to extract an upstream 3kb sequence from. I then want to run this upstream region through some TF prediction software to look fo ...
sequence written 5 weeks ago by a.rex150 • updated 5 weeks ago by Alex Reynolds25k
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How do I extract Fasta Sequences based on a list of IDs?
... I have a fasta sequence file that looks like this: >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3 MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY LKMKGDYFRYLSEVASGDNKQT ...
grep sequence written 7 weeks ago by a.rex150 • updated 7 weeks ago by Rashedul Islam290
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How find correlations between ChIP-seq tracks?
... I have two ChIP-seq tracks - specifically H3K4me3 and H3K27me3. I have used DeepTools to calculate coverage of each of the marks around annotated TSS's. How can I correlated between the two tracks at particular points around the TSS? i.e. I want an easy way to find genes that are represented at th ...
analysis chip-seq written 8 weeks ago by a.rex150 • updated 8 weeks ago by Rashedul Islam290

Latest awards to a.rex

Popular Question 5 weeks ago, created a question with more than 1,000 views. For parse error with samtools
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Student 5 weeks ago, asked a question with at least 3 up-votes. For mapping reads to repetitive elements in genome?
Popular Question 3 months ago, created a question with more than 1,000 views. For createRepeatLandscape in RepeatMasker
Popular Question 8 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Supporter 19 months ago, voted at least 25 times.
Student 20 months ago, asked a question with at least 3 up-votes. For mapping reads to repetitive elements in genome?

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