User: Lucila

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Lucila0
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Posts by Lucila

<prev • 8 results • page 1 of 1 • next >
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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 11 days ago by Lucila0
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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 3 months ago by Lucila0
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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 3 months ago by Lucila0
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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 4 months ago by Lucila0
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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 4 months ago by Lucila0 • updated 4 months ago by Brian Bushnell13k
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Minimum length in fastq quality trimmer with FASTX toolkit
... Hi all, I am filtering and trimming my RNA-seq data with fastq quality trimmer on FASTX toolkit, and I am wondering which minimum length I have to use, I mean, under which length it is convinient to discard the reads after the trimming. I have sequenced my samples with Illumina and my reads are 50b ...
quality filtering rna-seq written 4 months ago by Lucila0
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Comment: C: Incomplete titles in the BLAST output
... Thanks! And is there any similar tool to use with the query titles? To extract the query titles without spaces? ...
written 4 months ago by Lucila0
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Incomplete titles in the BLAST output
... Hi all, I need help with the BLAST output. The sequences of my database have spaces in the titles, and in the results the titles are shown until that space and I am losing the rest of the title. Is there any parameter or output format to use and obtain the complete titles in the output, without mod ...
blast written 4 months ago by Lucila0

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