User: GiusiG

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GiusiG0
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Posts by GiusiG

<prev • 5 results • page 1 of 1 • next >
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Infer experiment - Failed to determine strandin paired end stranded RNA-seq
... Hi, I'm having problems with a stranded, paired end RNA-seq analysis. I tried to map the reads with HISAT2 and RNA STAR but when I visualize the alignment it seems unstranded. If it helps, here the parameter I used with HISAT2: Tool Parameters Input Parameter Value Note for rerun ...
hisat2 paired end star rna-seq stranded written 12 weeks ago by GiusiG0 • updated 9 weeks ago by michael.ante3.0k
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eCLIP peak calling
... Hi everyone, I'm facing a problem calling peaks from a eCLIP experiment. I have 3 bam files: 2 replicates for one condition and a negative control. I don't know if this is the best option but I'm calling the peaks using MACS (from Galaxy), which is supposed to be for ChiP-seq and, for this reason, ...
macs peak calling clip galaxy written 3 months ago by GiusiG0 • updated 6 weeks ago by Ashley40
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Comment: C: MiRbase context IDs
... Actually, now that I think more about it, These transcript IDs from miRbase have to be the IDs of the miRNAs... Infact the FAQ I was referring to in the question was: " How can I get a list of intronic miRNAs?" http://www.mirbase.org/help/FAQs.shtml#How%20can%20I%20get%20a%20list%20of%20intronic%20m ...
written 4 months ago by GiusiG0
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Comment: C: MiRbase context IDs
... Thank you Emily, I thought these transcript ID from miRbase were the transcript IDs of the host genes... it makes sense what you explained! Thank you again ...
written 4 months ago by GiusiG0
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MiRbase context IDs
... Hello, I'm having troubles with the IDs in miRbase-context file. In particular, I have a list of around 300 miRNAs with a miRbase ID (i.e. hsa-mir-100). All I want to know is their genomic location: 3'UTR, Intron, Exon or 5'UTR. To do so, I downloaded from the FTP site of miRbase the file miRNA_co ...
mirbase ensembl id context rna-seq written 4 months ago by GiusiG0 • updated 4 months ago by Emily_Ensembl17k

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