read nanopore Fastq file
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@9d115a50
Last seen 6 weeks ago

Hi

what function I can use to read fastq file from Nanopore? My fastq file contain letter "U", so I cannot use ReadFastq() function from shortread library.

NanoporeRNASeq RNASeq • 95 views
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@james-w-macdonald-5106
Last seen 19 hours ago
United States

You don't say what you want to do once you read it in. But anyway.

> library(Biostrings)
## I modified the FASTQ file in the ShortRead dir
> readLines(gzfile("C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz"), 2)
[1] "@ERR127302.8493430 HWI-EUS350_0441:1:34:16191:2123#0/1"                  
[2] "GTCTGCTGTUTCTGTGTCGGCTGTCTCGCGGGACATGAAGTCAATGAAGGCCTGGAATGTCACTACCCCCAG"

## Note the U at pos 10

> z <- readRNAStringSet("C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz", "fastq")
Error in .Call2("read_fastq_files", filexp_list, nrec, skip, seek.first.rec,  : 
  reading FASTQ file C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz: line 2: read sequence contains invalid letters

## same error you get with ShortRead. Howeva

> z <- readBStringSet("C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz", "fastq")
> z
BStringSet object of length 20000:
        width seq                                           names               
    [1]    72 GTCTGCTGTUTCTGTGTCGGC...CTGGAATGTCACTACCCCCAG ERR127302.8493430...
    [2]    72 CTUGGGCAATCTTTGCAGCAA...AGGCCAGAGCAGACCTTCGGG ERR127302.2140653...
    [3]    72 TGGGCTGTTCCTTCTCUCTGT...AGAGTCACGTTTCCCAAGTCT ERR127302.2217310...
    [4]    72 CTCUTCCACACCTTTGGTCTT...CTCAGCATCAAAGTTAGTATA ERR127302.1040226...
    [5]    72 GTTTGGUTATATGGAGGATGG...ATAGGGCAAGGACGCCTCCTA ERR127302.1948626...
    ...   ... ...
[19996]    72 GCGGGUGCGGCCAAAATGAAG...AAGAATCGCAAAAGGCATTTC ERR127302.2468696...
[19997]    72 TTGTUATCTACTCTTGAACAA...GGCAGCTAATAGTGTGAACCA ERR127302.8014168...
[19998]    72 TGTTGUTGGTGCTGGTTACTG...AGTTACACACAGCCCTGCCTC ERR127302.1481100...
[19999]    72 CGGUGGTGCAGCCCCCGCCCA...ACCTGCCCGAGTTCATTGTGA ERR127302.1875050...
[20000]    72 GCUAGGGCGTCATGCTGGCCG...TCAACATCCCCAACGAGGACT ERR127302.1454058...

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