User: Katie __

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Katie __10
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Posts by Katie __

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Tru Seq small RNA library prep kit
... I ended up emailing illumina support and they said > TruSeq Small RNA produces stranded libraries. I believe the FAQ refers to the fact that the kit should not be used to produce stranded mRNA libraries with larger inserts, like the ones produced via TruSeq Stranded mRNA. ...
written 4 weeks ago by Katie __10
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Comment: C: Tru Seq small RNA library prep kit
... ok, thank you! ...
written 4 weeks ago by Katie __10
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Tru Seq small RNA library prep kit
... Hello! Could anyone help me determine if illumina Tru Seq small RNA kit is unstranded or stranded (first or second)? On [illumina support][2] is says tru seq small rna libraries cannot be used for directional RNA sequencing but this [post][1] quotes a paper that states it produces strand specif ...
illumina smallrna rna-seq sequencing written 4 weeks ago by Katie __10
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Comment: C: Small RNA Alignment
... The GENCODE website states the fasta file I used was a genome sequence, is this incorrect? Thank you for your help! ...
written 7 weeks ago by Katie __10
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Comment: C: Small RNA Alignment
... Ok thank you, I didn't realise that. I will try aligning to the whole genome (using GRCh38.p13 from GENCODE) and see if that improves my alignment. One of my problems was that neither Ensembl nor GENCODE list piRNA within their biotypes. Will using the whole genome for alignment mark these piRNA r ...
written 7 weeks ago by Katie __10
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Comment: C: Small RNA Alignment
... I had got previous advice suggesting to use the non-coding region of the genome and I used the ensemble ncRNA fasta sequence. Would you recommend aligning to the whole genome instead? I have 8 different small RNAs I'm looking at with this data so I wasn't sure what the best approach was for alignme ...
written 7 weeks ago by Katie __10
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Small RNA Alignment
... Hello! My dataset contains a number of smallRNAs and after alignment using bowtie with the non-coding region of the human genome (most recent version of HG 38) only 51% was aligned. I was wondering if I should maybe grep for example miRNA and piRNA first and align them to miRBase and piRbase respec ...
smallrna hg38 rna-seq bowtie sequencing written 7 weeks ago by Katie __10
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Comment: C: Small RNA seq analysis
... that's great, thank you! ...
written 9 weeks ago by Katie __10
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Comment: C: Small RNA seq analysis
... ok, just to double check, no merging across different flowcells? Also, if the sample libraries with different indexes are in different pools are these still considered library prep replicates? ...
written 9 weeks ago by Katie __10
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Comment: C: Small RNA seq analysis
... Thank you for the reply. I should have clarified earlier but the data I was given is a subset of a larger dataset where there are 19 pools with 45 samples within run on multiple flowcells and lanes. The data I was given was 27 FastQC files from within one pool. Is it still appropriate for me to merg ...
written 9 weeks ago by Katie __10

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