User: maria2019
maria2019 • 50
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Posts by maria2019
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... I believe not. The head of fastq file is as follow:
@NB551007:45:HNKVLBGX5:1:11101:18335:1071 1:N:0:GCCAAT
CTGGANGCGAGCCAACTGTAGGCACCATCAATNCCGTGCCCTCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEE#EAEEEEEEEE#EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE
@NB551007:45:HNKVLBG ...
written 8 days ago by
maria2019 • 50
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... I have single ended 75 bp miRNA reads (Quiagene miRNA kit) reads with UMI.
The fastqc report shows high peak at the 83-84 bp and illumina universal adaptor.
After removing the 5-3' adaptor ((5’-3’) AACTGTAGGCACCATCAAT) and also reads lower than 17bp with cutadapt, The sequence distribution peak i ...
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... I have one paired ended (150x2) WGS fastq file.
fastqc QC total read = ~ 459 M
fastqc QC after trimming total reads = ~ 458 M
after the alignment with bwa-mem and realigning around the indel, I used QUALIMAP for QC and the report shows ~723 M reads!
Why do I get more reads after the alignment?
...
written 11 days ago by
maria2019 • 50
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... Thank you very much Kevin, this was a huge help. ...
written 11 days ago by
maria2019 • 50
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... Hi Kevin,
I have done bulk RNA-seq DEG analysis.
I want to do the following analysis next:
a) miRNA DEG analysis ( i know how to do this step)
b) mRNA and miRNA integration analysis ( for this step, I need mRNA reads)
I want to know if I can analyze just mRNA DEG ( not bulkRNA). for that, I th ...
written 11 days ago by
maria2019 • 50
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... I want to filter mRNA and then perform 1. DEG analysis 2. integration analysis with microRNA.
My question is about how I can separate mRNA. I know the steps for 1 and 2. ...
written 15 days ago by
maria2019 • 50
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... I actually have a reference annotation. Awesome! thanks
...
written 15 days ago by
maria2019 • 50
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... I just read briefly about it. The description says that (The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.). Looks like it only removes rRNA? I know that rRNA is the majority of the rna found but how about other types of RNA? ...
written 15 days ago by
maria2019 • 50
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... Thank you very much. I'll try it ...
written 15 days ago by
maria2019 • 50
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... Hi,
I have Bulk RNA-seq and microRNA-seq read data of my samples. I wanna filter the bulkRNA-seq to get only the DEG for mRNA. after that, I am interested to work on the mRNA-seq and microRNA-seq data intergration analysis.
My question is, how can I filter bulkRNA-seq to get only mRNA reads? (usin ...
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For What is the right illumina universal adapter sequence for trimming paired-end reads?
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