User: Gema Sanz

gravatar for Gema Sanz
Gema Sanz30
Reputation:
30
Status:
New User
Location:
Karolinska Institutet
Last seen:
2 weeks, 2 days ago
Joined:
4 years ago
Email:
g*******@gmail.com

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Posts by Gema Sanz

<prev • 16 results • page 1 of 2 • next >
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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 21 days 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 21 days 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 21 days 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 21 days ago by Gema Sanz30 • updated 21 days ago by Asaf4.5k
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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 29 days 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 4 weeks 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 weeks ago by Gema Sanz30
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Comment: C: featureCounts reports zero counts when using GTF Repeatmasker track from UCSC an
... Thanks for your answer h.mon! In Bowtie2 I used default mode (search for multiple alignments, report the best one), I'm not sure what you mean with "keep only one copy of the repeat". Reads are mapped directly to repeat indices not to human genome. I think there is an option in featureCounts to keep ...
written 4 weeks ago by Gema Sanz30
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featureCounts reports zero counts when using GTF Repeatmasker track from UCSC and Bowtie2 SAM mapped RNA-seq reads
... Hi, I want to calculate the read counts mapping to repeats in my RNA-seq data. I mapped the reads using Bowtie2 to indices of repeats from UCSC Repeatmasker track in fasta format. Next, I have to calculate the read counts per repeat type, so I tried with featureCounts tool (in Galaxy server). But t ...
software error rna-seq written 4 weeks ago by Gema Sanz30
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Comment: C: Tools For Visualizing Overlap Between Go Terms
... the limit is 350 terms ...
written 5 months ago by Gema Sanz30

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For WGBS data analysis in Galaxy?

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