User: iraia.munoa

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iraia.munoa10
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Posts by iraia.munoa

<prev • 4 results • page 1 of 1 • next >
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Different options tryed with DiffBind and did not know what final result believe
... Hi all! I am working with ChiP-Seq data (Control and Treatment samples, with 2 replicates in each) and I have used DiffBind R package to finally obtain the differential binding sites. First of all I tryed with the protocol "DiffBind: Differential binding analysis of ChIP-Seq peak data" to see how ...
R diffbind deseq2 chip-seq edger written 3 days ago by iraia.munoa10
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RNA-seq samples along different time points, how to run Stringtie?
... Hi! I have a question about something similar. If I have 3 control and 3 treatment samples, each of one corresponding at a time point (24h 72h and 120h). How do you recommend to run strigtie? 1- If I want to compare in the differential expression analysis control and treatment in each time point do ...
stringtie rna-seq time-point written 12 weeks ago by iraia.munoa10 • updated 12 weeks ago by grant.hovhannisyan1.3k
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Different results when visualizing tdf files in IGV and when doing the differential expression analysis with ballgown
... Hi everybody, I am new with RNA-Seq bioingormatic analysis and I am having some troubles when comparing results from visualization and final Ballgown outputs. I have 6 RNA-Seq samples with two replicates for each one, and run in two different lines (So I have 4 fastq files for each sample). First ...
assembly ballgown rna-seq igv written 12 weeks ago by iraia.munoa10 • updated 12 weeks ago by RamRS19k
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Comment: A: Number of mapped reads from BAM file
... Hi! I have run bowtie2 for the alignment of my chip-seq files, and then run samtools view to convert the sam files in bam. Also I have run samtools sort, to sort the bam file and samtools index to index the bam file. > bowtie2 -q -x mm10_genome -U file_trimmed.fq -S file.sam --no-unal > samt ...
written 4 months ago by iraia.munoa10

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