tag:blogger.com,1999:blog-8584629468471803075.post3480748844261019667..comments2024-01-31T12:30:28.282+00:00Comments on Blasted Bioinformatics!?: FASTQ must die! Long live SAM/BAM!Peter Cockhttp://www.blogger.com/profile/00233221181317137855noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-8584629468471803075.post-29652848323678726652018-02-06T09:41:17.891+00:002018-02-06T09:41:17.891+00:00Hi Sayantan. I think you'd be better off askin...Hi Sayantan. I think you'd be better off asking on a more focused forum or Q&A site like https://www.biostars.org/ or http://seqanswers.com/forums/forumdisplay.php?f=18 - there is more than one way to do this. For example, the read quality checking tool FASTQC appears to take FASTQ, SAM or BAM as input http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - and personally I would have used the samtools fastq command to convert BAM into FASTQ if required.Peter Cockhttps://www.blogger.com/profile/00233221181317137855noreply@blogger.comtag:blogger.com,1999:blog-8584629468471803075.post-36731193230037347362018-02-06T04:39:54.592+00:002018-02-06T04:39:54.592+00:00Thanks for the interesting read. I have one questi...Thanks for the interesting read. I have one question. Recently I downloaded a WGS cancer dataset with matched normal/tumor pairs. All the files were in bam. Now I wanted to check the FASTQ quality that produced these bam files and so I first split them up into two reads (they were paired ended) using BEDTOOLS and checked their quality using FATSQC tool. IS this the right way to go about it?Anonymoushttps://www.blogger.com/profile/15025295677730357836noreply@blogger.com