User: Lucila

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Lucila10
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8 hours ago
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1 year, 3 months ago
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Posts by Lucila

<prev • 18 results • page 1 of 2 • next >
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Mapping reads against a de novo assembly -- no genome available
... Hi all, I have assembled a *de novo* transcriptome with Trinity and I was wondering which is the best approach to assess the differential expression of my samples. I have 2 conditions, with 4 replicates each, it means a total of 8 libraries with paired end reads that I used to make the assembly. I d ...
mapping differential expression written 1 day ago by Lucila10
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Comment: C: Trimmomatic error "Exception processing reads"
... I think that Trimmomatic can handle them. I have some but not a lot, since the fastqc report was good in that field. ...
written 4 months ago by Lucila10
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Comment: C: Trimmomatic error "Exception processing reads"
... Hi Pierre, thanks for your answer. I read that post before addying this one, but it seems that it is not my problem, since both files have all the reads with 150 bp length. ...
written 4 months ago by Lucila10
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Comment: C: Trimmomatic error "Exception processing reads"
... Thank you very much for your answer, and sorry about the mistake in the code format. In the Trimmomatic manual, it says it can handle the .gz extensions. Applying zmore to my files, it shows the following: ------> C1_USR16086979L-A69_HFKJWBBXX_L7_1.fq.gz <------ @K00124:558:HFKJWBBXX ...
written 4 months ago by Lucila10
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Trimmomatic error "Exception processing reads"
... Hi all, I am trying to run Trimmomatic but I obtained this error that I can not undestand: TrimmomaticPE: Started with arguments: -threads 20 -phred33 C1_USR1_1.fq.gz C1_USR1_2.fq.gz C1_trimmed.paired.1.fastq C1_trimmed.single.1.fastq C1_trimmed.paired.2.fastq C1_trimmed.single.2.fastq TRAILIN ...
trimmomatic written 4 months ago by Lucila10 • updated 12 weeks ago by Biostar ♦♦ 20
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Comment: C: Low percentage of mapped reads in TopHat
... Thank you genomax! I have done that. I don't know if I am using it correctly, first I indexed the genome: $ bbsplit.sh ref=genome.fasta usemodulo (I had to use usemodulo because I don't have enough memory in my machine) And then I've done this to find the reads that map to the genome: $ bbsplit.s ...
written 10 months ago by Lucila10
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Comment: C: Low percentage of mapped reads in TopHat
... It is indeed rRNA. And yes, I trimmed the adapters and check the quality of the reads before running TopHat. ...
written 10 months ago by Lucila10
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Comment: C: Low percentage of mapped reads in TopHat
... I did that and I do have contamination with Ribosomal RNA (not only of my organism of interest, also microbial ribosomal RNA). Do you have any ideas of why could this happen? Perhaps a problem during the preparation of the libraries? I would like to take out all these reads before making an assembly ...
written 10 months ago by Lucila10
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Comment: C: Low percentage of mapped reads in TopHat
... Thank you for your answer! No, I didn't check that. Which is the best way of doing that? Perhaps a BLAST using the ribosomal RNA sequence of a related species could work? Anyway, the reads that come from the Ribosomal RNA should also map to the genome, don't they? ...
written 10 months ago by Lucila10
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Low percentage of mapped reads in TopHat
... Hi all, I have a dataset of 14 million 50bp single-end reads (Illumina), and used Tophat to map them to a genome (indexed with Bowtie). I do not have the gff of the genome. When I ran it, only 50% of the reads were mapped. I have other libraries (a total of 200 million reads) of the same organism b ...
tophat bowtie rna-seq written 10 months ago by Lucila10

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