Question: SGSeq error on getBamInfo
0
gravatar for oolongoni
20 months ago by
oolongoni10
California
oolongoni10 wrote:

Hello,

I am running into some trouble using SGSeq::getBamInfo.

> getBamInfo(df)

Warning message:
Custom tag 'XS' not found in BAM file:
   ''

Spliced alignments must include a custom tag 'XS'.
Compatible BAM files can be obtained with an alignment
program for RNA-seq data (e.g. GSNAP, HISAT, STAR, TopHat). 

 

This is strange because I used STAR aligner and can see from samtools view output that the BAM files do in fact have the `Custom tag 'XS'` What could be the problem?

$ samtools view ~/scratch/NeoGeo/BAM/CD19/CD19_KTP-33_S14_L00.bam | head -10

NB501378:127:HL3WTAFXX:2:21104:15141:15869    163    chr16    28931963    255    75M    =    28932344    445    CCTGCGCGAAGCTGGGTGCCCCGGAGAGTCTGACCACCATGCCCCCTACTCGCCACCACTTCTTCCTCCGCTTCC    AAAAA6EEA/EAE6E6EEEEAEEEEEE/EEEA//E/AEE//EE/6EE/</E/<A/A//EEEAE<EA////EEA<E    NH:i:1    HI:i:1    AS:i:123    NM:i:5    MD:Z:43A3C6T2T11T5

NB501378:127:HL3WTAFXX:3:11602:9797:7135    163    chr16    28931984    255    76M    =    28932376    468    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAAEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE/EEEA    NH:i:1    HI:i:1    AS:i:150    NM:i:0    MD:Z:76

NB501378:127:HL3WTAFXX:1:11107:12902:5751    163    chr16    28931984    255    76M    =    28932376    468    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAAEEEEEE6EEEEEEEEEE/<EEEEEEEEEEAEEEEEEEEAEEAEEEEAEE/E/EAEEAE<EA<EEA</A/EA    NH:i:1    HI:i:1    AS:i:150    NM:i:0    MD:Z:76

NB501378:127:HL3WTAFXX:4:11410:13267:13851    163    chr16    28931984    255    76M    =    28932075    424    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAAEEEEEAAEEAAEAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE/EEEEEE/EEEEEA/AEEE/    NH:i:1    HI:i:1    AS:i:152    NM:i:0    MD:Z:76    XS:A:+

NB501378:127:HL3WTAFXX:2:11310:16325:17106    163    chr16    28931984    255    76M    =    28932375    467    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAAEEEEE//EAEEE6EEEE/EEEEEEEEEEAEAEEEEEAEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEAEEA    NH:i:1    HI:i:1    AS:i:150    NM:i:0    MD:Z:76

NB501378:127:HL3WTAFXX:3:21412:2893:17606    163    chr16    28931984    255    76M    =    28932075    424    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCACTACTTCCTCCTCTTCCTCACCCCCAAGGAAGACACGCC    AA/AAEA/EEEEE/E/EEA/EEE<EEEEEEEA</EE////E6EAA<<//E/<EE/EEEAAEEA/<EEE//AE/EEE    NH:i:1    HI:i:1    AS:i:140    NM:i:5    MD:Z:36T2T23T5T2G3    XS:A:+

NB501378:127:HL3WTAFXX:1:11306:16231:6320    163    chr16    28931984    255    76M    =    28932350    442    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE/E/EEEEEEEEE/EE<E//AEE    NH:i:1    HI:i:1    AS:i:150    NM:i:0    MD:Z:76

NB501378:127:HL3WTAFXX:4:11512:14545:4425    163    chr16    28931984    255    76M    =    28932362    453    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEA/EEEEEAEEE/EEAE<EEEE    NH:i:1    HI:i:1    AS:i:149    NM:i:0    MD:Z:76

NB501378:127:HL3WTAFXX:2:21304:13368:17224    163    chr16    28931984    255    76M    =    28932362    453    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAA/EEEAAEEE/EE/EEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEE6EEEEE/EEEEAEEEAEE<E</EE    NH:i:1    HI:i:1    AS:i:149    NM:i:0    MD:Z:76

NB501378:127:HL3WTAFXX:1:21106:16530:11344    163    chr16    28931984    255    76M    =    28932350    442    CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC    AAAAAEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEE/AEEEAEEEEEEEE    NH:i:1    HI:i:1    AS:i:148    NM:i:0    MD:Z:76
rnaseq sgseq getbaminfo • 389 views
ADD COMMENTlink modified 20 months ago by Leonard Goldstein80 • written 20 months ago by oolongoni10
Answer: SGSeq error on getBamInfo
1
gravatar for Leonard Goldstein
20 months ago by
United States
Leonard Goldstein80 wrote:

The error message should list the problematic files but it returns an empty string. Looks like something went wrong that was not caught by the internal checks (probably unrelated to the XS tag). Are your BAM file paths correct and are index files present? You can try running the following and see if you get a more informative error message

SGSeq:::getBamInfoPerSample(df$file_bam[1], NULL, df$sample_name[1])

 

ADD COMMENTlink written 20 months ago by Leonard Goldstein80
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