Hi guys,
I am new here. I am trying to use Bam2Fastq convert a very large (~7 GB) bam file to a fastq file, but whenever I try to do this, I get this weird message.
Basically I am trying to extract only aligned reads from a bam file, using this site as my guide: http://davetang.org/wiki/tiki-index....ls#Basic_usage
If that is not possible. If it is possible to convert the whole file to fastq will be good as well.
What I enter in Command Prompt
The message I get:
If you could kindly help. I will really appreciate it. Thank you.
-Zapages
I am new here. I am trying to use Bam2Fastq convert a very large (~7 GB) bam file to a fastq file, but whenever I try to do this, I get this weird message.
Basically I am trying to extract only aligned reads from a bam file, using this site as my guide: http://davetang.org/wiki/tiki-index....ls#Basic_usage
If that is not possible. If it is possible to convert the whole file to fastq will be good as well.
What I enter in Command Prompt
Code:
bam2fastq -o blah_aligned.fastq --no-unaligned Bamfilename.bam
Code:
The sequences in the BAM file are marked as Paired, but a single output file is specified. Ensure that the output filename (--output) includes a # symbol to be replaced with the read number
-Zapages
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