User: josmantorres

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josmantorres10
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Posts by josmantorres

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RNA-Seq Time series analysis in EdgeR
... Hello Biostars members, I have an RNA-Seq experiment from insect antennae across different data points (0,2,4,6 and 8 days) with 7 replicates per data point (except t6 with 6 replicates). I am analysing using EdgeR to identify differentially expressed genes. I have used the following EdgeR script in ...
R rna-seq edger written 9 months ago by josmantorres10
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Comment: A: Difference between mapped reads and counts
... Thanks for your quick answers and comments ! I will try HTseq and Featurecounts to obtain the count matrix instead of bedtools multicov Regarding Ian Sudbery's comment about gff3 filter, I used only gene lines, avoiding the problem with the isoforms. So, it could be a problem with bedtools multi ...
written 15 months ago by josmantorres10
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Difference between mapped reads and counts
... Hello Biostars members, I am analysing my RNA-seq data (20 M PE, 150 bp) using STAR (2.5V) to map the trimmed reads and "bedtools multicov" tool to obtain the transcript counts. After generating the genome index (the genome and GFF are available), I used the following STAR script to map my librari ...
rna-seq sequencing written 15 months ago by josmantorres10 • updated 15 months ago by _r_am31k
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Comment: A: Kmer content failed in FastQC analysis
... Thank a lot for you help and information ! It was very useful. As Michael said, viral load seems to be very high for me. It is possible that the presence of virus sequences makes that only 50% of the reads mapped against the genome? It is difficult to understand. Thanks again for your time and ...
written 2.2 years ago by josmantorres10
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Comment: A: Kmer content failed in FastQC analysis
... Thanks for your answer, As Macrogene made the sequencing and I paid for 20M and just 7.5 M mapped against the genome, I would like to know if the presence of genetic material from virus is normal in RNAseq experiments or is it possible that something wrong happened during the library preparation or ...
written 2.2 years ago by josmantorres10
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Comment: A: Kmer content failed in FastQC analysis
... Thanks a lot for your answer. As you suggested, I have made a blast against NCBI with the unmapped reads and they hit against Triatoma virus, which is present in the insect I have sequenced (https://en.wikipedia.org/wiki/Triatoma_virus). I think that this type of material would be eliminate during ...
written 2.2 years ago by josmantorres10
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Kmer content failed in FastQC analysis
... Hello, I have sent to sequence my RNAseq experiment to Macrogene. They used NovaSeq (Illumina Platform) to sequence my samples. I asked for 20M reads paired-end 150 bp length. I have made the FASTQC analysis of the raw reads and some samples showed strange Kmer-content graphs with an increase of sp ...
illumina rna-seq written 2.2 years ago by josmantorres10

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Popular Question 5 months ago, created a question with more than 1,000 views. For Kmer content failed in FastQC analysis

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