[Useq-users] Not mergeable SAM/BAM header constructed by SamTranscriptomeParser

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Hello Useq community,
I am trying to use Useq for RNAseq analysis with novoalignCS as the
aligner. My questions: How can I avoid this manual fixing of the header?
And how can I use the BAM file directly for STP?

Here are some information:

I produced each BAM file per lane for one sample. I used
SamTranscriptomeParser to convert the BAM file to chromosomes coordinates.
Here come my problems:

1. I can't use the BAM file directly for '-f' argument, I get around this
by converting the BAM file to SAM and feed it to STP. But I still wonder if
there is a way to use the BAM file directly.

2. I can't merge the BAM files after step 1. For example:
Sample1_Lane1.BAM, Sample1_Lane2.BAM, and Sample1_Lane3.BAM. The problem is
that the @SQ lines of these BAM files are different, both at SN and LN
values. If I do with test data of small number of reads, there are more
differences in SN values because STP throw away all chromosomes that do not
have reads. Below is first 30 lines from my RAW bam header, BEFORE the
conversion

@HD     VN:1.0  SO:unsorted
@PG     ID:novoalignCS  PN:novoalignCS  VN:V1.05.00     CL:novoalignCS -d
rn6.rnaseq.n60k.cnx -f L03.xsq -F XSQ LT2 -o SAM -r Random
@SQ     SN:chr1 LN:282763074    AS:rn6.rnaseq.cnx
@SQ     SN:chr2 LN:266435125    AS:rn6.rnaseq.cnx
@SQ     SN:chr3 LN:177699992    AS:rn6.rnaseq.cnx
@SQ     SN:chr4 LN:184226339    AS:rn6.rnaseq.cnx
@SQ     SN:chr5 LN:173707219    AS:rn6.rnaseq.cnx
@SQ     SN:chr6 LN:147991367    AS:rn6.rnaseq.cnx
@SQ     SN:chr7 LN:145729302    AS:rn6.rnaseq.cnx
@SQ     SN:chr8 LN:133307652    AS:rn6.rnaseq.cnx
@SQ     SN:chr9 LN:122095297    AS:rn6.rnaseq.cnx
@SQ     SN:chr10        LN:112626471    AS:rn6.rnaseq.cnx
@SQ     SN:chr11        LN:90463843     AS:rn6.rnaseq.cnx
@SQ     SN:chr12        LN:52716770     AS:rn6.rnaseq.cnx
@SQ     SN:chr13        LN:114033958    AS:rn6.rnaseq.cnx
@SQ     SN:chr14        LN:115493446    AS:rn6.rnaseq.cnx
@SQ     SN:chr15        LN:111246239    AS:rn6.rnaseq.cnx
@SQ     SN:chr16        LN:90668790     AS:rn6.rnaseq.cnx
@SQ     SN:chr17        LN:90843779     AS:rn6.rnaseq.cnx
@SQ     SN:chr18        LN:88201929     AS:rn6.rnaseq.cnx
@SQ     SN:chr19        LN:62275575     AS:rn6.rnaseq.cnx
@SQ     SN:chr20        LN:56205956     AS:rn6.rnaseq.cnx
@SQ     SN:chrX LN:159970021    AS:rn6.rnaseq.cnx
@SQ     SN:chrY LN:3310458      AS:rn6.rnaseq.cnx
@SQ     SN:Zbtb22:chr20:5478760-5478829_5479425-5479494 LN:138
 AS:rn6.rnaseq.cnx
@SQ     SN:Taf11:chr20:7477919-7477988_7482497-7482566  LN:138
 AS:rn6.rnaseq.cnx
@SQ     SN:Taf11:chr20:7477185-7477254_7478450-7478519  LN:138
 AS:rn6.rnaseq.cnx
@SQ     SN:Taf11:chr20:7478469-7478538_7480277-7480346  LN:138
 AS:rn6.rnaseq.cnx
@SQ     SN:Taf11:chr20:7477185-7477254_7477891-7477960  LN:138
 AS:rn6.rnaseq.cnx
@SQ     SN:Taf11:chr20:7480357-7480426_7482497-7482566  LN:138
 AS:rn6.rnaseq.cnx

And below is the header produced by STP after the conversion:

@HD     VN:1.4  SO:coordinate
@RG     ID:2.LT2.3      SM:LT2  CN:AfMD LB:LT2_2        PL:SOLiD
 PU:2.LT2.3
@SQ     SN:chr10        LN:112626471    AS:rn6.rnaseq.cnx
@SQ     SN:chr11        LN:90463843     AS:rn6.rnaseq.cnx
@SQ     SN:chr12        LN:52716770     AS:rn6.rnaseq.cnx
@SQ     SN:chr13        LN:114033958    AS:rn6.rnaseq.cnx
@SQ     SN:chr5 LN:173707219    AS:rn6.rnaseq.cnx
@SQ     SN:chr6 LN:147991367    AS:rn6.rnaseq.cnx
@SQ     SN:chrY LN:3310458      AS:rn6.rnaseq.cnx
@SQ     SN:chr7 LN:145729302    AS:rn6.rnaseq.cnx
@SQ     SN:chr8 LN:133307652    AS:rn6.rnaseq.cnx
@SQ     SN:chr9 LN:122095297    AS:rn6.rnaseq.cnx
@SQ     SN:chrX LN:159970021    AS:rn6.rnaseq.cnx
@SQ     SN:chr15        LN:111246239    AS:rn6.rnaseq.cnx
@SQ     SN:chr14        LN:115493446    AS:rn6.rnaseq.cnx
@SQ     SN:chr17        LN:90843779     AS:rn6.rnaseq.cnx
@SQ     SN:chr16        LN:90668790     AS:rn6.rnaseq.cnx
@SQ     SN:chr19        LN:62275575     AS:rn6.rnaseq.cnx
@SQ     SN:chr1 LN:282763074    AS:rn6.rnaseq.cnx
@SQ     SN:chr18        LN:88201929     AS:rn6.rnaseq.cnx
@SQ     SN:chr2 LN:266435125    AS:rn6.rnaseq.cnx
@SQ     SN:chr3 LN:177699992    AS:rn6.rnaseq.cnx
@SQ     SN:chr4 LN:184226339    AS:rn6.rnaseq.cnx
@PG     ID:SamTranscriptomeParser       CL: args [12 Mar 2015 9:53]
USeq_8.8.9 -f LT2.2.LT2.3_unsorted.fifo.sam -a 900 -n 100 -u -s
LT2.2.LT2.3_unsorted.tmp.bam
@PG     ID:novoalignCS  PN:novoalignCS  VN:V1.05.00     CL:novoalignCS -d
rn6.rnaseq.n60k.cnx -f L03.xsq -F XSQ LT2 -o SAM -r Random

As you may see, the canonical chromosomes got reordered, chromosome 20 is
thrown out. If I have @RG lines, they would be thrown out also.
I can extract the header I want to use from the raw bam file: samtools view
-H raw_alignment.bam| egrep -v  "@SQ\s+SN:[A-Za-z0-9]+:.*$|@HD". Then I can
add the header with:

 "SamTranscriptomeParser -f test.sam -s test.bam -h head.txt "

Thanks
Vang