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fastest solution to get bam2fastq done memento Bioinformatics 34 05-31-2014 03:51 AM

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Old 04-19-2012, 08:20 AM   #1
wangli
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Location: Texas

Join Date: Apr 2012
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Default bam2fastq

I installed the software bam2fastq to convert my bam file into fastq format.

[li@raven D0AJWACXX_6]$ bam2fastq -o allreadsFBK04#.fastq INX730_D0AJWACXX_6_AAACAT.bam
This looks like paired data from lane 6.
Output will be in allreadsFBK04_1.fastq and allreadsFBK04_2.fastq
120443552 sequences in the BAM file
120443552 sequences exported

From the output above, it seems everything works all right. But after it is done, I cannot find the output file in the directory or any other folder in my computer.

Any comments will be very appreciated. Thank you in advance!
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