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distinguish the paired-end reads #1

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zhangzhiyangcs opened this issue Aug 3, 2021 · 2 comments
Open

distinguish the paired-end reads #1

zhangzhiyangcs opened this issue Aug 3, 2021 · 2 comments

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@zhangzhiyangcs
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zhangzhiyangcs commented Aug 3, 2021 •
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Hi,
I have some questions:

  1. I have many samples. if I merge two fq in one fq for each samples, it will cost many time and disks. Do you have any suggestion to improve the command "sed 's/ /_2 /' FASTQ2|cat FASTQ1 - > merge.fastq" that I can imput 1.fq.gz and 2.fq.gz directly.
  2. Why use tophat2 instead of STAR or hisat2?
  3. I have annoted 2400 cscRNAs in one sample. Is there an scripts to filter the false positive cscRNAs?
    Best wish
@zhangzhiyangcs zhangzhiyangcs reopened this Aug 4, 2021
@wyt14
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wyt14 commented Apr 24, 2022

we test result: tophat2 has the relativelay high accuracy.

@wyt14
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wyt14 commented Apr 24, 2022

The filter script will be updated soon~

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@wyt14 @zhangzhiyangcs