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**GenoMax** · 01-15-2014, 06:05 AM

If this is TCGA RNA-seq data from UNC then the following would work. Send me a PM if you have any problems.

In certain circumstances, a small fraction of the sequences and quality scores in these reads are rearranged such that they cannot perfectly reconstruct the original fastq record. To remedy this error we have provided fastq files to CGHUB.

OR

A sam2fastq option is available in UBU version 1.2. It is only properly tested against Mapsplice paired end.

Sample usage:

Code:

$ java -Xmx512M -jar ubu.jar sam2fastq --in sorted_by_name.bam --fastq1 1.fastq --fastq2 2.fastq --end1 /1 --end2 /2

The input BAM should be sorted by name. i.e. with "samtools sort -n"

The standalone jar file ubu-1.2-jar-with-dependencies.jar is available from the UBU downloads page:

https://github.com/mozack/ubu/downloads

**fulvio.dan** · 01-16-2014, 12:33 AM

Thanks GenoMax! You are right!
They are TCGA RNA-Seq data, and ubu sam2fastq worked!

**jstjohn** · 06-04-2015, 08:00 AM

UBU likes only paired reads in the BAM files

In case this helps anyone else: when I was converting TCGA RNA-seq reads to fastq format UBU complained about the presence of unpaired reads. The following was my workaround.

Split paired and unpaired bam records.

Code:

samtools  view -b -U unpaired.bam -o paired.bam  \
        -@ 3  -f 1 \
        $BAM

Sort paired reads by name.

Code:

samtools sort \
        -n -o namesort.bam  -T namesort_pre -@ 3 -m 3G -O bam \
        paired.bam

Run UBU sam2fastq on paired namesorted reads, outputing --fastq1 and --fastq2

Code:

java -jar -Xmx512m ubu-1.3-SNAPSHOT-jar-with-dependencies.jar sam2fastq \
        --in namesort.bam \
        --fastq1 r1.fastq \
        --fastq2 r2.fastq \
        --mapsplice

Run UBU sam2fastq on unpaired reads, outputting --fastq1 only into an unpaired fastq file.

Code:

java -jar -Xmx512m ubu-1.3-SNAPSHOT-jar-with-dependencies.jar sam2fastq \
        --in  unpaired.bam  \
        --fastq1 fu.fastq \
        --mapsplice

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Converting RNA-Seq bam in fastq

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