User: Seq225
Seq225 • 50
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Posts by Seq225
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... 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 20 days ago by
Seq225 • 50
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... 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 21 days ago by
Seq225 • 50
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... 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 ...
written 21 days ago by
Seq225 • 50
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... Thanks you very much ...
written 21 days ago by
Seq225 • 50
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... 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 23 days ago by
Seq225 • 50
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... 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 ... ...
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... Great. Thank you!
I will try these... ...
written 7 weeks ago by
Seq225 • 50
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... Its ok. Thanks very much Ram!! ...
written 7 weeks ago by
Seq225 • 50
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... Thanks very much. I will replace the print with qx.
Also, if you don't mind and have time to spend, is it possible to point out the other problems?
Thanks like a ocean!! ...
written 7 weeks ago by
Seq225 • 50
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... I am very confused here. I think the main execution here is based on the perl script. I have provided it below.
The entire idea is to extract sequences with “Complete Proteome” in the Keyword from files downloaded (Swiss-Prot and TrEMBL).
All I am trying to do is repeating some analyses from this ...
written 7 weeks ago by
Seq225 • 50
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For De Novo Assembly of small RNA Reads (Illumina)
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