User: Rogerio Ribeiro

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Posts by Rogerio Ribeiro

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Answer: A: About alignment rate of Dendrobium officinale (a plant) used RSEM software
... There could be a number of reasons. I would start to perform a QC on the data (check if adaptors were correctly removed; base quality etc). It would probably help if you posted the RSEM command you used (I have no experience with RSEM but other users might). ...
written 24 days ago by Rogerio Ribeiro30
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Comment: C: Estimaing insert size from a pair-end library using bbmap
... I meant the `pairlen=` option. I've checked this link here [http://seqanswers.com/forums/showpost.php?p=158099&postcount=2][1] and I ran the the bbmap command as follows: bbmap.sh ref=cro_genome.fasta in1=R1.pair.fastq.gz in2=R2.pair.fastq.gz -ihist=ihist.txt reads=1M maxindel=200000 pai ...
written 28 days ago by Rogerio Ribeiro30
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Comment: C: Estimaing insert size from a pair-end library using bbmap
... Hi again. It seems I forgot one important detail in the question. The data comes from RNA-seq data. I believe since there could be introns, the min length should be decreased. Or maybe should I used an entirely different tool. Sorry about that it has been a long day ...
written 29 days ago by Rogerio Ribeiro30
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Comment: C: Estimaing insert size from a pair-end library using bbmap
... okay I tested two settups: Original untrimmed data with merge: bbmerge.sh in1=R1.untrimmed.fastq.gz in2=R2.untrimmed.fastq.gz reads=2m ihist=ihist.txt Pairs: 2000000 Joined: 674961 33.748% Ambiguous: 1323904 66.195% No Soluti ...
written 29 days ago by Rogerio Ribeiro30
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Comment: C: Estimaing insert size from a pair-end library using bbmap
... Its a draft genome still, with 2090 contigs, from the same species. BBMAP is able to map around 95% of the reads. I have obtained the same values with illumina ...
written 29 days ago by Rogerio Ribeiro30
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Comment: C: Estimaing insert size from a pair-end library using bbmap
... Yes I forgot to paste the ref= option. Why use original data instead of data without adaptors? (just for reference, only a small amount of reads pairs are discarded after trimmomatic filters by size. I seems however that the pairlen=2000 option is important. Here is the reestimation: Mean 392.9 ...
written 29 days ago by Rogerio Ribeiro30
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Estimaing insert size from a pair-end library using bbmap
... Hi biostars. I'm trying to estimate the insert size of a pair-end illumina library. I have limited information about library preparation and sequencing protocol (2x125). To estimate the insert size I used mapped the reads to a genome using bbmap. The reads were processed using trimmomatic (to remo ...
bbmap rna-seq written 29 days ago by Rogerio Ribeiro30
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Comment: C: Question regarding minimap2 presets
... Yes, my long reads spawn from 50 bps to 30 kps, with the most of them being in (roughly) between 350-900. I think that most of my data is not complete transcripts, based on the read size compared to the average predicted gene size in my species. Furthermore, the RIN values from my samples were mostl ...
written 5 weeks ago by Rogerio Ribeiro30
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Question regarding minimap2 presets
... Hi biostars. I have a question regarding minimap2. For my biological problem, I am doing differential expression analysis and differential transcript usage for six (3 vs 3) samples, which have been sequenced using a cDNA protocol with MinIOn. To start I built a genome-guided transcriptome using m ...
minimap2 alignment rna-seq written 6 weeks ago by Rogerio Ribeiro30
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Hybrid transcriptome assembly
... Hi all. For my project, I have been working with Illumina RNA-seq samples and a genome assembly of my species, and one of my tasks was to improve the genome annotation and build a genome-guided transcriptome for my species. For this purpose, I used hisat2 + stringtie2. Recently, it has been made ...
illumina stringtie nanopore rna-seq written 6 weeks ago by Rogerio Ribeiro30

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