User: Lucila

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Lucila10
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8 months, 2 weeks ago
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Posts by Lucila

<prev • 13 results • page 1 of 2 • next >
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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 3 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 3 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 3 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 3 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 3 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 4 months ago by Lucila10
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Preprocessing RNA-seq data with BBDuk
... Hi all, I am preprocessing my data with BBDuk and have some doubts regarding adapter-trimming. I want to delete all the sequences of adapters and primers from both ends of my reads. When I run BBDuk with ktrim=r and then the result with ktrim=l, I do not obtain the same result (for example, the num ...
adapter trimming bbduk quality trimming rna-seq written 7 months ago by Lucila10
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Comment: C: Minimum length in fastq quality trimmer with FASTX toolkit
... Thank you Brian for your response. Regarding the histogram, which software do you recommend to plot it in a graph? I have visualized more than one peak with FASTQC. So perhaps it could be interesting to assemble them independently. Which tool allows me to organize the reads according to the GC cont ...
written 7 months ago by Lucila10
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Comment: C: Minimum length in fastq quality trimmer with FASTX toolkit
... Thanks for your answer st.ph.n. Unfortunately we only have these single-end reads 50 bp lenght. Do you think it is possible to make a de novo assembly with them? We selected the cheaper option but maybe it was not the best.... ...
written 8 months ago by Lucila10
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Comment: C: Minimum length in fastq quality trimmer with FASTX toolkit
... Thanks Brian, 1- The organism is Triatoma infestans, an insect vector belonging to subfamily Triatominae (Hemiptera, Reduviidae). We do not have the genome, so we do not have information about its size and GC content. This organism is diploid. 2- Regarding the experiment, we want to quantif ...
written 8 months ago by Lucila10 • updated 8 months ago by Brian Bushnell14k

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