Entering edit mode
6.4 years ago
landrjos
▴
20
Hi All,
I use Bowtie2 to align my Illumina Fastq sequence files then convert to BAM using Samtools. The BAM output file does not have any barcode information. Or any @RG information at all. Here is the header from one of the BAM files....
Does Bowtie2 save this information? If so I would I access it from the BAM file?
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:197195432
@SQ SN:chr2 LN:181748087
@SQ SN:chr3 LN:159599783
@SQ SN:chr4 LN:155630120
@SQ SN:chr5 LN:152537259
@SQ SN:chr6 LN:149517037
@SQ SN:chr7 LN:152524553
@SQ SN:chr8 LN:131738871
@SQ SN:chr9 LN:124076172
@SQ SN:chr10 LN:129993255
@SQ SN:chr11 LN:121843856
@SQ SN:chr12 LN:121257530
@SQ SN:chr13 LN:120284312
@SQ SN:chr14 LN:125194864
@SQ SN:chr15 LN:103494974
@SQ SN:chr16 LN:98319150
@SQ SN:chr17 LN:95272651
@SQ SN:chr18 LN:90772031
@SQ SN:chr19 LN:61342430
@SQ SN:chrX LN:166650296
@SQ SN:chrY LN:15902555
@SQ SN:chrM LN:16299
@SQ SN:chr13_random LN:404305
@SQ SN:chr17_random LN:628739
@SQ SN:chr1_random LN:1231697
@SQ SN:chr3_random LN:41899
@SQ SN:chr4_random LN:160594
@SQ SN:chr5_random LN:357350
@SQ SN:chr7_random LN:362490
@SQ SN:chr8_random LN:849593
@SQ SN:chr9_random LN:449403
@SQ SN:chrUn_random LN:5900358
@SQ SN:chrX_random LN:1785075
@SQ SN:chrY_random LN:58682461
@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
HWI-ST425:160:D1JFWACXX:3:1306:14534:76146 16 chr1 3000195 42 36M * 0 0 GTATTATAATTGTAATAGTATATACTTGTATGTACT JJJJJJJJJJJIJJJJJJJJJJHFHHHHFFFFFBCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:MD:Z:36 YT:Z:UU
HWI-ST425:221:C6B83ACXX:8:1201:13332:28408 0 chr1 3000206 42 36M * 0 0 GTAATAGTATATACTTGTATGTACTTAAAATATTTT CBCFFFFDHHHHHJJJJIJJJJJJJJJJJJJJJJJJ AS:i:-4 XN:i:4 XM:i:4 XO:i:0 XG:i:0 NM:i:MD:Z:32N0N0N0N0 YT:Z:UU
HWI-ST425:221:C6B83ACXX:8:1113:12482:87912 0 chr1 3000818 42 36M * 0 0 CTATCATGACCTCTGAATGACTAGGGAATCTTGGAC @@@FFDFFHHHHHJJIGIJCHGHHGGIEHHGGIIIJ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:MD:Z:36 YT:Z:UU
HWI-ST425:221:C6B83ACXX:8:2309:10001:51423 0 chr1 3000818 42 36M * 0 0 CTATCATGACCTCTGAATGACTAGGGAATCTTGGAC CCCFFFFFHHHHHJJJJJJIIJJJJJJJIJJJJGIJ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:MD:Z:36 YT:Z:UU
Did you provide the read group information to bowtie2? If so, show the parameters you used.
Here is the script I am using to run Bowtie2....Where would I add the read group information?
Right, so you didn't tell it to use any read group information.
I am not a professional. Could you suggest some changes to the script to retain the read group information?
Have you read the bowtie2 documentation? Do so first, this is documented there.