User: maria2019

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maria201950
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Posts by maria2019

<prev • 42 results • page 1 of 5 • next >
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Comment: C: miRNA fastqc sequence length distribution with UMI
... 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 maria201950
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miRNA fastqc sequence length distribution with UMI
... 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 ...
qiagene trimming fastqc mirna cutadapt written 8 days ago by maria201950 • updated 8 days ago by swbarnes26.7k
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why my WGS bam file (after alignment) shows more reads than the starting fastq file
... 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? ...
total read wgs qualimap qc fastqc written 11 days ago by maria201950
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... Thank you very much Kevin, this was a huge help. ...
written 11 days ago by maria201950
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... 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 maria201950
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... 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 maria201950
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... I actually have a reference annotation. Awesome! thanks ...
written 15 days ago by maria201950
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... 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 maria201950
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... Thank you very much. I'll try it ...
written 15 days ago by maria201950
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Can I filter mRNA from bulk RNA-seq reads?
... 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 ...
mrna-seq bulk rna-seq written 15 days ago by maria201950 • updated 15 days ago by elsoja70

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