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I am entirely new to using sequence and alignment files. Is there a way to convert .BAM to FASTA or FASTQ?
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Not sure if this is the easiest way, but I use BBTools's reformat.sh along with samtools for that.
reformat.sh in=reads.bam out=reads.fq
That requires samtools to be in your path. -
There's also SamToFastq from Picard tools (contrary to its name, it supports BAM files too).Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.Yesterday, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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