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Old 09-07-2017, 04:42 AM   #5
anotherSAM
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Location: Paris

Join Date: Sep 2017
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Code:
head -n1 test.sam 
m54072_170901_055052/5112430/0_2238	4	*	0	255	*	*	0	0	TTCCGGGGATGGGGGGTCTTGGTATTGGACATCTATATGGTTCCTTTCCACTAAACTTGAGGCATCAGGCCTGTTTGGACCGGAGTACGTAAATTTCGTTTTCGTTATTTTCGATCCATGGCTCATTCTTCGTTGGCGCTTTTCTATCAAGAGATGAGGAACCAGCTCTACTCTATGTT	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	bc:B:S,1,1	bq:i:85	cx:i:10	ip:B:C,1,61,22,90,8,8,72,3,7,40,9,68,4,15,8,12,72,34,156,61,10,3,50,9,70,74,16,17,2,28,6,38,60,13,11,13,122,14,42,70,7,12,14,32,25,21,38,14,7,8,34,2,1,7,5,12,60,61,6,5,8,9,52,3,16,182,7,86,44,15,56	np:i:1	pw:B:C,7,5,13,13,2,11,2,5,6,10,3,6,47,13,24,41,7,6,7,6,39,34,12,44,5,11,18,21,8,15,14,7,7,2,6,5,8,30,28,3,4,2,22,15,12,13,4,15,2,12,10,7,8,17,5,9,2,22,26,24,7,13,11,6,9,6,6,10,3,11,3,3,14,6,4,17,10     qe:i:2238	qs:i:0	rq:f:0.8	sn:B:f,7.81349,14.5671,6.42793,10.4147	zm:i:5112430RG:Z:25f8c430
Brian, This is what the respective sam file looks like (i removed the majority of the nucleotides, numeric values and exclamation points for better clarity).
Sklages, This is with sequel data, however if it is true that the bam files do not have a quality score, where is it? From what I had read, the new bam output was meant to replace fastq.
Genomax, I followed the link for installing the bam2fastx library tool, which considering no error messages occurred I thought had succeeded, but when I went to use the bam2fastq command, it was unavailable.

Thank you all for your replies

Last edited by GenoMax; 09-07-2017 at 04:57 AM. Reason: more clarity; added [CODE] tags
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