User: corend

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corend70
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Posts by corend

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Comment: C: Parsing RepeatMasker Output Files
... Maybe you can check : http://doua.prabi.fr/software/one-code-to-find-them-all ...
written 2.1 years ago by corend70
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Comment: C: bedtools intersect with match on name column
... My bad, my example was not a MWE, I will validate your answer. If you replace 10 25 by 10 35 here you will see the problem. ...
written 2.2 years ago by corend70
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Answer: A: bedtools intersect with match on name column
... I finaly found out how to do it: As I want a Chromosome and name match, I just make a bedfile in the format `chr+name start end name`, and it works well. ...
written 2.2 years ago by corend70
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Comment: C: bedtools intersect with match on name column
... Sorry, it is not working, here is the problem: In the second step, you don't intersect line by line, so the problem is still the same. Just try it and you will see. ...
written 2.2 years ago by corend70
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bedtools intersect with match on name column
... I have files `a.bed` and `b.bed` `a.bed` chr1 10 20 geneA chr1 30 40 geneB `b.bed` chr1 5 15 geneA chr1 10 25 geneB if I `intersectbed` those files I will obtain: chr1 10 15 geneA chr1 10 20 geneA But I would like the `name` column to match between files so that i wil ...
bedtools intersectbed written 2.2 years ago by corend70
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Comment: C: What is the ideal FDR and fold change cutoff to consider in a RNA-seq experiment
... You should definitely use a threshold on both metrics. Depends on how many DEGs you want to retrieve, take a look at the litterature, which thresholds are used in other papers. Then look how many DEGs you have with those thresholds and modify if necessary. Also you should consider for the Fold ch ...
written 2.4 years ago by corend70
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Comment: C: Mapping to repeat consensus sequences?
... I am not a ChIP seq specialist. But my personal point of view would be to do the peak calling, and then compare to the repeatmasker gff. ...
written 2.4 years ago by corend70
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Comment: C: Mapping to repeat consensus sequences?
... Repeat modeler finds the repeated sequences in the genome. It gives them a number (your x), and compares them to repbase. If the sequence has a hit, it is annotated with the hit in repbase. > How can I obtain consensus sequences for LTRs or specific families of LTRs? The consensi.fa file alread ...
written 2.4 years ago by corend70
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Answer: C: isolate the output of lignment in fastq format
... https://www.biostars.org/p/770/ ...
written 2.4 years ago by corend70
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Comment: C: Detection Transposable Elements in eukaryote
... Is it repeat modeler or repeat masker that do not find them? Repeat modeler only finds what is repeated. If a LTR is old and present in only one copy, it might remain undetected by repeat modeler. Then you should use LTRharvest that uses the structure of the LTR to detect it and not it's repeated na ...
written 2.4 years ago by corend70

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Popular Question 3 months ago, created a question with more than 1,000 views. For A very short gene with very high TPM
Popular Question 10 months ago, created a question with more than 1,000 views. For bedtools intersect with match on name column
Popular Question 10 months ago, created a question with more than 1,000 views. For A very short gene with very high TPM
Popular Question 12 months ago, created a question with more than 1,000 views. For Why does cufflinks split this transcript?
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Popular Question 20 months ago, created a question with more than 1,000 views. For Why does cufflinks split this transcript?
Popular Question 20 months ago, created a question with more than 1,000 views. For A very short gene with very high TPM
Popular Question 21 months ago, created a question with more than 1,000 views. For A very short gene with very high TPM
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Scholar 2.2 years ago, created an answer that has been accepted. For A: bedtools intersect with match on name column
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