Some "QNAME" information lost after mapping by Bsmap

[illuminaGA]

Dear All

I mapped my bisulfited DNA sequencing reads by Bsmap, the out put file was SAM format. Before that, I trimmed 18bp repeat reads.But after mapping, some information in the "QNAME" lost.

Here is an example

Trimmed reads mapping

ILLUMINA-XXXXX3:7:FC665XXXXXX:1:1 345 chr17 7111078 255 51M * 0 0 ACACACATACATACACACATACACAGGCCTTCACCAAACACACCCAACGNA BGDGDGGGEGGDDGDGEGGGEHHHHHGGGGGGFGGGGGGGG7<>7>>>(#> NM:i:10 ZS:Z:-+

unTrimmed reads mapping

ILLUMINA-XXXXX3:7:FC665XXXXXX:1:18:11311:15796 153 chr19 42422318 255 101M * 0 0 TGGTGTATGTGGGGTGTACACATACCTCTCATGTATACGCCACATATACACCACACATACCACATATACACACCACAGACAAACCAAACACACCCAACACA DG@BDBBCACFF@FDFFBF3324*53/)'*315/HGEIHDBBDDDBIDI?CC@<EGDECGDBGGDGGBEBG>GG@<BGDFIIEIIIIIIIIHIIIIIIGII NM:i:13 ZS:Z:+-


The red part lost in the sam file which generated by trimmed reads. So someone know what happen here?

Any help would be greatly appreciated!

[Brian Bushnell]

What tool/command did you use for trimming? And can you paste a read from the trimmed fastq? It sounds like you're trimming headers in addition to bases.

[illuminaGA]

What tool/command did you use for trimming? And can you paste a read from the trimmed fastq? It sounds like you're trimming headers in addition to bases.

Thank you for replying.

The trimmed fastq reads are followed.

@ILLUMINA-8XXXXX:7:FCXXXXXAXX:1:1:6136:1035 1:N:0:GTGAAA
GTACCTGTGTAAGTGTATGCATGTATGCGAATGTATGTGTATGTGCATGTGAATGTATGTATGTGTGTATGTGCA
+
GGGGGGGGGGGGGDIIGIGIIIIHBEGEG>GGEG<GGDDD@GB@G?<G@B@;-BDEDEDGDDG?GG,E@=F##

@ILLUMINA-8XXXXX:7:FCXXXXXAXX:1:1:7632:1039 1:N:0:GTGAAA
TGTTGGGTGTGTTGGGTGTGTTGGGTGTGTGTGTGTGTGTGTGTGTGTGGTGTGTGGTGTGTGTGTGTGTGTGTGCGGTGTGTGTGTGTGTGTGTGTGT
+
C>CEF?BBGGGGEGGGDGDGGGGGGDGGGGGGGGGGGDGEGCGDGGGDGGGDGG>EFAECGCFEFCDCEFE>F3B6?BDD@BD0@=0=,B=B=2=B?BB
@ILLUMINA-8XXXXX:7:FCXXXXXAXX:1:1:6672:1077 1:N:0:GTGAAA
ATGTGTATGTATGTATGTATGTGTATGTGTGTATATGTGTGTGTATGTGTGTATATGTGTGTGTGTGTGTGTTGA
+
DGGGGDGGGFGGGGBHGHHHHGHHBGGBGEGD>GBGGEGEGEGEGGGBDDGDD>GGGDGBGBGDGDGBGBG>EGD
@ILLUMINA-8XXXXX:7:FCXXXXXAXX:1:1:15911:1085 1:N:0:GTGAAA
GTTGGGTGTGTTTGGGTTTGTGGTGTGTTGTGTGTGTATGTATGCATGTGTGTTTATGTGTTGTTATCTTCACATTTGTATGATTCATGCGGGCTGTCT
+
@A@=@<7@>B=;3EA7EEGGGGGE?EDDEEB?EGG=GGEB<>E3=@BAG?DB<:>ACBB=EE:/+@=4@;.40-5258;>+CA;?=:B###########

@ILLUMINA-8XXXXX:7:FCXXXXXAXX:1:1:18002:1087 1:N:0:GTGAAA
TGTTGGGTGTGTTGGGTGTGTATGTATGTGTATGTGTGTATATGTGTGTGTATGTAGTTTCAAAAACATACGCCCAAGACCACAAGTACAGATACATCT
+
B?BFFFEBGGGGGDGG8GGGGGGGGGGGGGGGGHHHHHHHH?GHHHEHGHHG@GGGGFEGG?DGDGEAAGB:BCEDE?F=AF@BBD?D8FFD#######

@ILLUMINA-8XXXXX:7:FCXXXXXAXX:1:1:7076:1090 1:N:0:GTGAAA
GGGTGGATTGAAGCATGGAATATATAGATTCAAATATGGGTCACACACACAGCTGCCACCCGCCAGTATCTGAAG
+
@?D5=@=BDDBDDDDDDD<DD@D<DDBDD@DD6BB4B@>BDB:?=4B=?@DBB0ABDD@)4912>B>:B*<=D

We write a code by Python to trim the repeat reads. We didn't remove any info. from the fastq title line.

I just guess something wrong in the format.

Thanks a lot!