Question

How To Convert Eland File To Bam?

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13.5 years ago

Zack ▴ 10

Does anyone know if it is possible to convert Eland file to BAM?

next-gen sequencing bam • 5.9k views

ADD COMMENT • link updated 13.3 years ago by lieyanfengbao ▴ 10 • written 13.5 years ago by Zack ▴ 10

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There is no such thing as an ELAND file. There are files created by ELAND or ELAND2. What is the extension of the file? is it a fastq file is it an export file? are there more than one files? Is this from a paired end or a single end sequencing project?

ADD REPLY • link 13.5 years ago by Biomed 5.0k

score 1 · Answer 1 · 2010-10-26

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13.5 years ago

Ian 6.0k

Samtools http://samtools.sourceforge.net/ includes a script called export2sam.pl. I have not used it myself, but its use is mentioned here: http://genomewiki.ucsc.edu/index.php/ABRF2010_Tutorial, under 'Viewing alignments in BAM format'.

You would then use: samtools view -bS -o out.bam in.sam

ADD COMMENT • link 13.5 years ago by Ian 6.0k