Hi all,
I generated some sam files with vDjer and wanted to apply these files to
RSEM.
To this end, I used commands as below:
(1) samtools-0.1.19/samtools view -1 -bS vdjer.sam > vdjer.bam
(2) samtools-0.1.19/samtools view -H vdjer.bam > vdjer.namesort.sam
(3) samtools-0.1.19/samtools view vdjer.bam | tr '\t' '~' | paste - - |
sort -S 3G | awk '{print $1 "\n" $2}' | tr '~' '\t' >> vdjer.namesort.sam
(4) samtools-0.1.19/samtools view -bS vdjer.namesort.sam >
vdjer.namesort.bam
There were no error in step (1), (2) and (3). Then, in step (4), I got an
error like this:
"*Parse error at line 24: sequence and quality are inconsistent*
*Aborted (core dumped)*".
Here is the line 24 in my vdjer.namesort.sam file:
SRRXXXX.16743551 99 vjf_13_TGTGCGAGGTTTATGATTACCTTTGCGGGGGAAGCTTTT
GATATCTGG 193 255 76M = 276 159
TCTGTGACCGCCGCAGACAC
GGCCGTATATTACTGTGCGAGGTTTATGATTACCTTTGCGGGGGAAGCTTTTGATA
@@@DDBBDFHHHHI8)CG GIDHAF6?AFGGHGIIIFEEHGEHEEEEECCD@;@CCCCC@BBB7@>B<8@
@@CA<CCSRR2780299.16743551 147
vjf_13_TGTGCGAGGTTTATGATTACCTTTGCGGGGGAAGCTTTTGATATCTGG 276 255
76M = 193 159 CCAAGGGAGAATGGTCACCGTCTCTTCAGCCTCCACCAAGGGCC
CATCGGTCTTCCCCCTGGCGCCCTGCTCCAGG
DDDDDDDEDDCCDC?<);DDDBDCCDDDB?A;;;;ECFFFHF
EHA<HJIJIHF<IHGEEADIIHDHHHDFDADC@@
Could anyone help me out?
Looking forward your reply.
Best,
Yue
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