User: Apprentice

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Apprentice40
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Posts by Apprentice

<prev • 61 results • page 2 of 7 • next >
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Comment: C: How to trim poly-sequence before or after trimming by Trimmomatic.
... I would like to remove polyA tails using prinseq. My RNA-seq data is paired end. My fastq files were gzipped. It seems that prinseq can't read gzipped fastq files. I don't want to decompress the fastq files. Could you tell me how to use prinseq for paired-end gzipped fastq files? ...
written 13 months ago by Apprentice40
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Comment: C: How to trim poly-sequence before or after trimming by Trimmomatic.
... Thank you for your advice. I'll try it. ...
written 13 months ago by Apprentice40
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Comment: C: How to trim poly-sequence before or after trimming by Trimmomatic.
... Thank you for you comment. I don't know how sequence should be added to the file as the polyA and polyT. Could you tell me examples of the file? ...
written 13 months ago by Apprentice40
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How to trim poly-sequence before or after trimming by Trimmomatic.
... Hi. I'm analyzing RNA-seq data. My pipeline of RNA-seq was as below. (1) Trimmomatic exclude adapter sequences and low-quality bases from my fastq files. (2) Tophat2 mapped my reads to the reference sequence (hg19). Trimmomatic didn't remove poly-A sequence from my fastq files. I would like to ...
rna-seq written 14 months ago by Apprentice40 • updated 14 months ago by WouterDeCoster44k
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Comment: C: Why are there many reads with green color in IGV of RNA-seq data?
... Thank you for your advices! I'll carefully check sequence data from my bam files. ...
written 15 months ago by Apprentice40
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Comment: C: Why are there many reads with green color in IGV of RNA-seq data?
... Thank you for your editing. About the trimming and mapping, my commands are as below. ----------------------------------------------------------- java -Xmx4g -jar trimmomatic-0.38.jar PE -threads 1 -phred33 -trimlog ${id}.trimlog \ ${id}_R1.fastq.gz ${id}_R2.fastq.gz \ ${id}_R1.paired.fastq.gz ${i ...
written 15 months ago by Apprentice40
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Comment: C: Why are there many reads with green color in IGV of RNA-seq data?
... I'm sorry for my late reply. I've uploaded a part of image when my bam file was shown by IGV. ![enter image description here][1] I feel that there are many green reads in the bam file. If you notice something bout the image, please tell me. [1]: https://i.ibb.co/wBXcGN8/image.png ...
written 15 months ago by Apprentice40 • updated 15 months ago by Charles Warden7.9k
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Comment: C: Why are there many reads with green color in IGV of RNA-seq data?
... Thank you for your advice. Could you tell me how to check whether there are the ribosomal RNAs? Should I check whether tandem repeats were mapped in my bam file? ...
written 15 months ago by Apprentice40
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Comment: C: Why are there many reads with green color in IGV of RNA-seq data?
... Thank you for your comment. I resubmitted my comment under the answer of dario.garvan. ...
written 15 months ago by Apprentice40
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Comment: C: Why are there many reads with green color in IGV of RNA-seq data?
... Thank you for your comment. As you said, tophat 2 is an old method. So, I tried to apply HISAT2 into same fastq file. As a result, the bam file indicated similar result that there were many green reads. ...
written 15 months ago by Apprentice40

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