User: Lucila

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Lucila10
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11 months, 1 week ago
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Posts by Lucila

<prev • 17 results • page 1 of 2 • next >
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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 25 days 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 25 days 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 25 days 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 25 days ago by Lucila10 • updated 25 days ago by genomax42k
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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 6 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 6 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 6 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 6 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 6 months ago by Lucila10
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Comment: A: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... Hi CandiceChuDVM, thank you so much for this post. It will be very useful. I would like to ask you one question: Do you know if they have requirements to let you upload you data (in terms of quality and contamination of your samples, for example with adaptors)? Thank you! Cheers, Lucila. ...
written 7 months ago by Lucila10

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