Dear all,
I'm trying to generate a BAM files from the SAM output of Bowtie2.
However I obtain the following error message:
My script is the following:
And my SAM file look-like good :
I wonder if the problem come from the @ that is located just before the beginning of my reads ID.
Does anyone know how I can remove this @ from my sam file or have another idea?
Jeremie
I'm trying to generate a BAM files from the SAM output of Bowtie2.
However I obtain the following error message:
HTML Code:
expected '@XY', got [@HWI-ST610:134:C089FACXX:2:2308:274
5:149689 1:N:0:TGACCA%0ATAAAGATTAGGCAAGTTTGTGCTAATTTATAACTGTTTTTGAATGGAGGTGTAACA
ATACAAATACAAGTTTTGTGATAGATTATC%0A+%0AHHBFHFHHHIIHBCCA@F<CCGGE?D?BF@FDAEDF>GBGHBB
BCCHCH5@.@8=D@CCEHHE>CHD?DCDBCAA;A((5;@;A>@%0A]
Hint: The header tags must be tab-separated.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
HTML Code:
/usr/local/bin/samtools view -bS /home/jeremie/pdacidLT/reference/8.1_r1.sam > /home/jeremie/pdacidLT/reference/8.1_r1.bam
HTML Code:
@HD VN:1.0 SO:unsorted
@SQ SN:Locus_1685_Transcript_1/2_Confidence_1.000_Length_7457_transcripts_v2_1|spectrin LN:7457
[...the list of all my contigs ~70000]
@PG ID:bowtie2 PN:bowtie2 VN:2.0.5
@HWI-ST610:134:C089FACXX:2:2208:17424:162295 1:N:0:ACAGTG%0AGCGAGGGGACACATCGAAACATAATCCTGGCTTGATCTTCTGCGGGAAGAGGATGGAGACATTTTGATGGCAA
CGAATTCACGAAT%0A+%0AJJJJJJIJIIJJJJJJJJJJIIGFHJGEIGGJIJGIIGIHHHFHFDBB?=AB<?C?AACBCACDED?:@>CCDBB@8??CA>ABBB%0A
@HWI-ST610:134:C089FACXX:2:2208:17424:162295 2:N:0:ACAGTG%0AGCGGGCTAGGTTTGTACAGCAGTCCAAATCGTCGTCTCCCAGGCAGCTGAGAACCACAGAAAGTGCGTTGCCA
AACAAACCAGACA%0A+%0AGGHJGIJJJJ8@FHHJJJGIIHGHHHEFFFFDDCDB?CDDCDDDDDDDDDDCDDB@BBDDDDAACDD?@DDDDDDDD?BB@ABDDD%0A
HWI-ST610:134:C089FACXX:2:2208:17409:162308 83 transcripts_v2_656|kruppel-like 1108 255 86M = 1074 -120TTACCAAGTATGGTATTGCCAGTGTCAACTGTGAGCACAGCAACATTACCCACTGGTACACAATCAGTACATTCATGATTATGTAA CA;@CCECDFFDFHHHHHIHGGIHCIJJJJJJJJIIIJJIJJIIG
GHHIJIHGGHHEIIGIJJIJIIGHJIGIJJJJJJIJJJJJJ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:86 YS:i:0 YT:Z:CP
@HWI-ST610:134:C089FACXX:2:2208:17409:162308 1:N:0:ACAGTG%0ATTACATAATCATGAATGTACTGATTGTGTACCAGTGGGTAATGTTGCTGTGCTCACAGTTGACACTGGCAATA
CCATACTTGGTAA%0A+%0AJJJJJJIJJJJJJIGIJHGIIJIJJIGIIEHHGGHIJIHHGGIIJJIJJIIIJJJJJJJJICHIGGHIHHHHHFDFFDCECC@;AC%0A
HWI-ST610:134:C089FACXX:2:2208:17409:162308 163 transcripts_v2_656|kruppel-like 1074 255 86M = 1108 120 CACACAGCAGCCTATGCAAATTACAAGTAACTCTTTACCAAGTATGGTATTGCCAGTGTCAACTGTGAGCACAGCAACATTACCCA JJJJJJJIJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJIJJFHI
JJFFHIIHIJJGHIJIGJHHEHFHFFFFFDEEECD@CDDDD AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:86 YS:i:0 YT:Z:CP
@HWI-ST610:134:C089FACXX:2:2208:17409:162308 2:N:0:ACAGTG%0ACACACAGCAGCCTATGCAAATTACAAGTAACTCTTTACCAAGTATGGTATTGCCAGTGTCAACTGTGAGCACA
GCAACATTACCCA%0A+%0AJJJJJJJIJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJIJJFHIJJFFHIIHIJJGHIJIGJHHEHFHFFFFFDEEECD@CDDDD%0A
Does anyone know how I can remove this @ from my sam file or have another idea?
Jeremie
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