User: shuchen

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shuchen10
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Posts by shuchen

<prev • 17 results • page 1 of 2 • next >
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GATB-CORE set up in LoRDEC
... I am installing LoRDEC for long read correction. Following is the installation instruction of LoRDEC. I am having trouble with the 4th step. Could anyone give me some advice? Thank you so much! 1. Unpack LoRDEC-0.6.tar.gz. 2. cd LoRDEC-0.6 3. Download the GATB Core library from http://gatb-cor ...
gatb-core variable lordec long read correction written 6 months ago by shuchen10 • updated 6 months ago by Biostar ♦♦ 20
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Answer: A: use proovread to correct Pacbio reads with Illumina reads
... Also,when I designated multiple illumina fastq files, it seems that proovread only use the first fastq file for the correction. Do I need to merge all the fastq files before running proovread? Or I am not using proovread right? ...
written 6 months ago by shuchen10
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use proovread to correct Pacbio reads with Illumina reads
... I am trying to use proovread to correct Pacbio reads with Illumina reads. However, this process costs a very long running time. Is there any way to accelerate this process? I am thinking to normalize the read depth to 30X. Will this significanlt shoreten the running time? Hope there is someone had e ...
proovread illumina pacbio correction written 6 months ago by shuchen10
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Comment: C: fastqc: kmer-content failed
... I blasted the unmapped reads and it turned out a lot of them are 100% similar to ecoli genes, so I am a little confused why it did not map to the ecoli genome at the first place. ...
written 6 months ago by shuchen10
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Comment: C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
... Thank you! I think this is a possible reason for that. I will check with the sequencing company if they did some enrichment. ...
written 7 months ago by shuchen10
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Comment: C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
... Thank you. I will check some similar experiments of similar species. ...
written 7 months ago by shuchen10
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Is it normal to have low expression levels of house keeping genes in plant RNA-seq results
... We had a RNA-seq experiment for a plant material (no genome reference available), 6 samples, 3Gb Illumina Hiseq PE reads for each sample. The transcriptome reference was constructed with Trinity and then the reads of each sample were aligned to this constructed reference with Bowtie2. The overall a ...
low expression level house keeping gene rna-seq written 7 months ago by shuchen10
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Comment: C: fastqc: kmer-content failed
... I was using a SRA dataset which is an isolate. So what do you think might be the problem? I am not very familiar with bacteria. Is it possible that E. coli DNA sequence is very different between strains and caused this low alignment rate. ...
written 7 months ago by shuchen10
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Comment: C: fastqc: kmer-content failed
... I aligned the reads towards an e. coli genome downloaded from NCBI using bowtie2, --very-sensitive-local, but only got 66.91% overall alignment rate. Is this alingment rate normal? 1593573 reads; of these: 1593573 (100.00%) were paired; of these: 570107 (35.78%) aligned concordantly 0 t ...
written 7 months ago by shuchen10
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Comment: C: fastqc: kmer-content failed
... Ok. Thanks. I will try it on a computer with larger memory. ...
written 7 months ago by shuchen10

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