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User: Seq225

gravatar for Seq225
Seq225 • 70
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Posts by Seq225

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Problem mapping mRNA seq data using STAR.
... I think you can change it. I guess the default is 60. Please check their manual. ...
written 5 weeks ago by Seq225 • 70
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Comment: C: Which metagenomics tool works best?
... Great! Thanks. I will use both then. ...
written 5 weeks ago by Seq225 • 70
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Comment: C: Which metagenomics tool works best?
... Thank you. I have actually read this today. Looks like I can use either one. ...
written 7 weeks ago by Seq225 • 70
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Which metagenomics tool works best?
... Hi, I have paired end illumina reads from multiple sources. I want to study the metagenomics. Which tool would be best? I can see people are using MEGAN, Kraken, Centrifuge more than the other tools. My main objective is to compare the metagenomics population across my samples. Thanks! ...
genome assembly metagenomics alignment sequencing written 7 weeks ago by Seq225 • 70
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Comment: C: Very low mapping rate of mRNA seq data
... ATpoint and Mehemt, thank you very much. I have talked with the sequencing core. They never depleted the rRNA. That could be the actual problem. Do you guys know any way to find out the rRNA mapping percentage of my data? Like I said, I do not have a genome sequence for this organism. Is there any ...
written 11 weeks ago by Seq225 • 70
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Comment: C: Very low mapping rate of mRNA seq data
... Thank you. The reads are good quality (almost all of them). Not sure about any sort of contamination. Unfortunately, I do not have a ref genome. ...
written 11 weeks ago by Seq225 • 70
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Very low mapping rate of mRNA seq data
... Hi, I have ~100 paired end mRNA seq data (150 Nt read size) that were sequenced by Illumina MiSeq. I have clipped the adapter by cutadapt. I am getting low mapping percentage. I used BWA, Bowtie2, and STAR. For STAR, I am getting 3-30% mapping. Bowtie2 ~40% and BWA 40-45%. I am using assembled tran ...
genome assembly rna-seq sequencing written 11 weeks ago by Seq225 • 70
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Comment: C: Problem mapping mRNA seq data using STAR.
... Thanks you very much ...
written 11 weeks ago by Seq225 • 70
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Comment: C: Problem mapping mRNA seq data using STAR.
... There are some 0 nt reads. I am sure about that. STAR (or any other aligner probably) had problem working on 0 nt reads. I am asking if they have resolved that issue? Or I have to delete those reads from my file. ...
written 11 weeks ago by Seq225 • 70
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Problem mapping mRNA seq data using STAR.
... I am running STAR on paired end reads:** star --runThreadN 50 --genomeDir index --readFilesIn ASS_1_1.fq.gz ASS__1_2.fq.gz --outFileNamePrefix ASS.mapped.sam --readFilesCommand gzcat Sep 21 16:20:32 ..... started STAR run Sep 21 16:20:33 ..... loading genome Sep 21 16:20:39 ... ...
assembly alignment rna-seq written 11 weeks ago by Seq225 • 70 • updated 6 weeks ago by Biostar ♦♦ 20

Latest awards to Seq225

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