User: Lila M

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Lila M 230
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230
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Location:
UK
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2 days, 4 hours ago
Joined:
1 year, 6 months ago
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Posts by Lila M

<prev • 127 results • page 1 of 13 • next >
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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... I'm reading it! Thank you very much :) ...
written 16 days ago by Lila M 230
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Comment: C: compare peaks in a gene list (coordinates)
... I have two files ( a and b), both are BED files (chr, start, end, strand) of different transcripts. I would like to compare them in therms of peaks, so I would like to know the number of peaks in **file a** and the number of peaks in **file b** to compare. So I don't know how I can get the number o ...
written 17 days ago by Lila M 230
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compare peaks in a gene list (coordinates)
... Hi everybody, I have a bed file with coordintes and the name of the transcript for each coordinate. I would like if there is any way for getting the peaks over this bed file. Can MACS2 do this? Thanks! ...
gene bed peaks chip-seq written 17 days ago by Lila M 230 • updated 17 days ago by vchris_ngs2.9k
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Comment: C: CpG islands density calculation
... Hi, as all the sequences have the same length (1,000 nt) I don't have to normalize for length. I downloaded the sequences for USCS, how can I know if they are directional? Thanks for the tips! ...
written 18 days ago by Lila M 230
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CpG islands density calculation
... Hi everybody, I downloaded the promoter sequences fortwo gene list using USCS, so I have all the fasta files stored in a txt file (file_a and file_b). I would like to know if there is any difference for the CpG in both files. To do that, I've performed a little code in R fastaFile_a = readDNA ...
promoters rna-seq cpg written 19 days ago by Lila M 230
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Comment: C: how to identify TATA box in a gene list
... As I said previously, I don't have any sequence, I only have gene IDs ...
written 20 days ago by Lila M 230
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Comment: C: how to identify TATA box in a gene list
... Thank you very much for the information! :) ...
written 20 days ago by Lila M 230
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Comment: C: how to identify TATA box in a gene list
... You are right, but for me "higher scores are better matches" is not much informative (what is considered higher and lower?, how can I set a proper cut-off? in my opinion there is not much information and is a bit complicate be sure about the result... ...
written 20 days ago by Lila M 230
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Comment: C: how to identify TATA box in a gene list
... The output of the result! As in it I can see the sequence, is not exactly the TATA sequence (I don't know if HOMER only report the most similar one) so How can be sure that the genes that the output report has TATA boxes? GeneID PromoterID Offset Sequence Motif Name Strand MotifScore Unigene R ...
written 20 days ago by Lila M 230
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Comment: C: how to identify TATA box in a gene list
... I think that is not necessary, If I downloaded the matrix from HOMER (paste above), is can be recognized. ...
written 20 days ago by Lila M 230

Latest awards to Lila M

Centurion 4 weeks ago, created 100 posts.
Supporter 6 weeks ago, voted at least 25 times.

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