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Hi all, I am PhD 1st year student, Now working with the high thoughput sequencing data file to search SNPs. I am working with SAM extension file of Chromosome 1 by using IGV 2.0 software. Can anyone give some idea how to convert SAM file to MUT or BED file? I am not sure whether there is any way or not. Regards, Maruf
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samtools to go from sam to bam, bedtools bamToBed to go from bam to bed. -
Hi mgogol,
Thanks for your reply.
where I can get the sam tools or bedtools? How about MUT files?
As mentioned earlier I am IGV 2.0, I tried by using RUN igvtools. I could convert SAM to tdf /idx/sai extension files only.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.07-01-2026, 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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