fetch_reads_from_fastq {chimeraviz} | R Documentation |
This function will fetch read sequences from fastq files and put them into new fastq files.
fetch_reads_from_fastq(reads, fastq_file_in1, fastq_file_in2, fastq_file_out1, fastq_file_out2)
reads |
List of read IDs that is to be fetched. |
fastq_file_in1 |
First fastq file to search in. |
fastq_file_in2 |
Second fastq file to seach in. |
fastq_file_out1 |
First fastq file with results. |
fastq_file_out2 |
Second fastq file with results. |
Note: This function runs (read only) bash commands on your system. Therefore the function will only work on a unix system.
The files fastqFileOut1 and fastqFileOut2 populated with the specified reads.
## Not run: # fastq files that has the supporting reads fastq1 <- system.file("extdata", "reads.1.fq", package="chimeraviz") fastq2 <- system.file("extdata", "reads.2.fq", package="chimeraviz") # Which read ids to extract reads <- c( "13422259", "19375605", "29755061", "31632876", "32141428", "33857245") # Extract the actual reads and put them in the tmp files "fastqFileOut1" and # "fastqFileOut2" fastqFileOut1 <- tempfile(pattern = "fq1", tmpdir = tempdir()) fastqFileOut2 <- tempfile(pattern = "fq2", tmpdir = tempdir()) fetch_reads_from_fastq(reads, fastq1, fastq2, fastqFileOut1, fastqFileOut2) # We now have the reads supporting fusion 5267 in the two files. ## End(Not run)