User: giorgiocasaburi

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Posts by giorgiocasaburi

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Merge fastq file from same lane and start bowtie alignment
... Nevermind it's actually working, my bad! Thank you so much for you help! ...
written 17 months ago by giorgiocasaburi90
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Comment: C: Merge fastq file from same lane and start bowtie alignment
... Not working, thank you though! ...
written 17 months ago by giorgiocasaburi90
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Comment: A: Merge fastq file from same lane and start bowtie alignment
... No one can answer this? ...
written 17 months ago by giorgiocasaburi90
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Comment: C: Merge fastq file from same lane and start bowtie alignment
... Right, but I have multiple files in different folders. So I was planning to just run the same script in every folder. That's why I was looking for something that could also write the output as i% based on the input name, otherwise I have to manually edit every time the script according to input. ...
written 17 months ago by giorgiocasaburi90
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Comment: C: Merge fastq file from same lane and start bowtie alignment
... I know that the original files will still be there, but the combined file (which is the all point of this post) is not appearing at this stage. ...
written 17 months ago by giorgiocasaburi90
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Comment: A: Merge fastq file from same lane and start bowtie alignment
... Thanks genomax, and sorry for the missing format. I am still having the issue of not being able to see a concatenated .gz file. I rather have this: L16-24MG-A_S14_L001_R1_001.fastq.gz L16-24MG-A_S14_L002_R1_001.fastq.gz.gz L16-24MG-A_S14_L004_R1_001.fastq.gz L16-24MG-A_S14_L001_R1_001.fastq ...
written 17 months ago by giorgiocasaburi90
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Merge fastq file from same lane and start bowtie alignment
... Hi all, I am trying to do a couple of operations in automatic. Basically I have a directory of fastq PE files from the same sample e.g.: L16-24MG-A_S14_L001_R1_001.fastq.gz L16-24MG-A_S14_L003_R1_001.fastq.gz L16-24MG-A_S14_L002_R1_001.fastq.gz L16-24MG-A_S14_L004_R1_001.fastq.gz ...
bowtie rna-seq written 17 months ago by giorgiocasaburi90
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Transcriptome hybrid assembly 454 + Illumina
... Hello,   I have tons of data (about 1Tb) of RNA-Seq coming from different technologies (i.e. 454 - single end, Illumina both single and paired end) of the same non-genome annotated species from different tissues/conditions. So far for the illumina data I did several assemblies with Trinity, specif ...
assembly transcritpome rna-seq written 3.3 years ago by giorgiocasaburi90
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Transcriptome Annotation for public database search
... Hi all, I have an assembled transcriptome (Trinity) and I am about to perform annotation. My goal is to basically made this a public database were people can blast their sequences against. Is there any tool that beside performing regular annotation, would also change the name of the header of the c ...
annotation database rna-seq transcriptome written 3.3 years ago by giorgiocasaburi90
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Comment: C: Trinity assembly validation and statistics
... Sorry I mean unique file as one merged with the R1 reads and another merged with the R2 reads. I did use left and right obviously. The goal is indeed compare the treatment so I would stuck with the pooling approach. I am currently running the assembly again using normalization and -min_kmer_cov 1. I ...
written 3.4 years ago by giorgiocasaburi90

Latest awards to giorgiocasaburi

Popular Question 3.2 years ago, created a question with more than 1,000 views. For Optimizing De Novo Transcriptome assemblies for non model organisms
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Trinity assembly validation and statistics

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