User: Gema Sanz

gravatar for Gema Sanz
Gema Sanz30
Reputation:
30
Status:
New User
Location:
Karolinska Institutet
Last seen:
3 days, 10 hours ago
Joined:
4 years, 3 months ago
Email:
g*******@gmail.com

about me

Posts by Gema Sanz

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Primer design to do qPCR on repetitive elements
... Thanks! I'm not looking for an unique amplicon, I want to amplify all the possible locations that can contribute to expression, I'm using Repbase consensus sequence, but somehow when checking all the possible matches with in silico PCR, for some repeats I don't get any results. ...
written 3 days ago by Gema Sanz30
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Primer design to do qPCR on repetitive elements
... Hi, I need to design qPCR primers to amplify some human repetitive elements. I'm using Primer BLAST and I wonder if there are any specific parameters to take into account to design them, i.e., Specificity check, Database... I removed the repeat filter but I'm not sure that the primer pair that I'm ...
repeats repetitive elements qpcr written 3 days ago by Gema Sanz30 • updated 3 days ago by trausch830
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Comment: C: Transform a GTF file into a data frame in R
... This worked for me thanks! Really helpful :) ...
written 5 weeks ago by Gema Sanz30
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Comment: C: How to introduce a spacer in a transcription factor PWM matrix?
... To do the same, but creating 18 instead of 15. ...
written 3 months ago by Gema Sanz30
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Comment: C: How to introduce a spacer in a transcription factor PWM matrix?
... I checked your suggestion but I think is not exactly what I want to do. The approach that I want to follow is described in one paper as follows: > The position weight matrix (PWM) from the Jaspar database19 described the p53 binding motif, composed by two decameric half sites. In order to accoun ...
written 3 months ago by Gema Sanz30
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Comment: C: How to introduce a spacer in a transcription factor PWM matrix?
... Thanks for your answer! I will take a look ...
written 3 months ago by Gema Sanz30
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How to introduce a spacer in a transcription factor PWM matrix?
... Hi, I need to modify the PWM matrix of a certain transcription factor to allow a spacer of different length, i.e., from 1 to 20 nucleotides, in a matrix like this for example: A [13006 75198 0 0 4556 0 74715 8654 60151 99494 0 ] C [10026 5868 0 0 0 994 ...
sequence written 3 months ago by Gema Sanz30 • updated 3 months ago by Asaf4.6k
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Comment: C: Salmon/Sailfish for repeat element quantification?
... I solved it, the TE gtf file didn't contain info for class and family, I used the file TE hg19_rmsk_TE.gtf provided in testdata_GTF folder and worked perfectly. ...
written 3 months ago by Gema Sanz30
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Comment: C: Salmon/Sailfish for repeat element quantification?
... Hi, I'm trying to use you tool TEcount in my RNA-seq data using this code: TEcount -b file.bam --GTF hg19UCSC.gtf --TE hg19repeakmasker.gtf --prefix outputfile but I get this error: chr1 hg19_rmsk exon 10001 10468 1504.000000 + . gene_id "(CCCTAA)n"; transcript_id "(CCCTAA)n"; TE GTF format ...
written 3 months ago by Gema Sanz30
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Answer: A: featureCounts reports zero counts when using GTF Repeatmasker track from UCSC an
... I tried the -M option in featureCounts (allow multi-mapped) but still I'm getting zeros everywhere: Geneid example.sam AluSp 0 AluY 0 L2b 0 L1PA10 0 L1PA2 0 L1MB7 0 ERVL-E-int 0 GTF repeatmasker file looks like this: Seqname Source Feature Start End Score Strand F ...
written 4 months ago by Gema Sanz30

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