User: Nunu
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Posts by Nunu
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... Hello community,
I'm using SPAdes to do de novo transcriptome assembly using RNA-seq (from Illumina). However, the new version SPAdes 3.14.1 has excluded the read error correction step for RNA-seq. So I want to use the BayesHammer which comes with SPAdes to do the error correction. However, I can't ...
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... Hello. Thanks for your help!
I'm using codeml to test patterns of selection among different species with a group genes. I have noticed in many research paper that genes need to be filtered with dn/ds>3 or ds<0.01 which will make the analysis inaccurate. In my case, I have noticed this problem ...
written 8 months ago by
Nunu • 0
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... I'm at the stage of trimming my codon sequences for codeml and I want to trim it using Trimal.
However, I can't find any option in trimal to indicate the format of the sequences. Alternatively, Trimal can align for protein sequences, but there is no option to get which sites were trimmed out, which ...
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C: trim galore for 10Xgenomics
... thanks. I will use Supernova. Do I need to do trimming first? In my file, there are 3 files, one index file and one paired end read files. I only have one sample, so I don't need to care about the index file and just proceed with the paired end reads. Is this correct? After checking supernova, I wil ...
written 15 months ago by
Nunu • 0
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C: trim galore for 10Xgenomics
... Thanks, do you know what should I do with these indexes? Also, do I need to figure out first the diploidy state of my targeted species to use a certain assembly software? ...
written 15 months ago by
Nunu • 0
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C: trim galore for 10Xgenomics
... hi, thanks a lot for the information. Yes, I'm doing de novo assembly. I have checked this website but it seems that they only recommend using supernova for diploid species, and mine is not diploid.. So I have to try using other assembly pipelines. The targeted genome is around 1Gb, for now, I want ...
written 15 months ago by
Nunu • 0
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C: trim galore for 10Xgenomics
... Thanks a lot! My data is genomics data from protozoa, so I can't follow single cell RNA seq pipelines. I only have one folder since it's sequenced long time ago but another technician. I used the following to check the index file
bioawk -cfastx '{print($seq)}' mysample_I1_001.fastq.gz | \
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... Hello helpers, I just got raw reads from 10Xgenomics and started to do trimming and assembly. I’m new to this technology and have some basic questions below. Basically, I want to use software trim galore for trimming first and have clarify these first so as to choose proper options.
1, I only have ...
written 15 months ago by
Nunu • 0
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