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Sam file manipulation

Hello All,

I have a standard SAM output from the HISAT2 splice aware aligner. I want to add the Query hit index tag to the output, which indicates position of the alignment record in SAM file. Is there a way to do that? The dataset is 50 bp SE RNA-Seq reads mapped to the genome using HISAT2

Thank you Abhijit

rna-seq format manipulation
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written by abhijit.synl abhijit.synl

Could you post the results of:

samtools view file.bam | head

And:

samtools view file.bam | grep "HI:i" | head

edit: by the way, why do you want the query hit index?

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written by h.mon h.mon

I want to use the program TransComb. It needs Tophat2 output with the Hit Query index field. Hisat2 does not give that. Here is the output. I am masking the reads cuz data is proprietary

34768728/1      256     N1      29379   1       50M     *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      BCCCCGGGGGGGGGGGGGFGGEEGGGGGGGGGGGGGGGGGGGGGGGGGGG     AS:i:0   ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:50 YT:Z:UU NH:i:4  RG:Z:AD941-1_2_3
35483537/1      256     N1      29383   0       4S46M   *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      BCC?AGGGGGGGGGGGGGFGGGGGGG@FGGGCGGGGGGGGGGFCGGGGGG     AS:i:-4  ZS:i:-4 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:46 YT:Z:UU NH:i:4  RG:Z:AD941-1_2_3
23926598/1      0       N1      33547   1       50M     *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      BBCBBFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG@CFGGGGGGGGGG     AS:i:0   ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:50 YT:Z:UU NH:i:2  RG:Z:AD941-1_2_3
32994362/1      256     N1      33938   1       33M     *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN       CCCCCGGGGGGGGGGGGGGGGGGGGG>>F<11>       AS:i:0  ZS:i:0  XN:i:0  XM:i:0 XO:i:0   XG:i:0  NM:i:0  MD:Z:33 YT:Z:UU NH:i:2  RG:Z:AD941-1_2_3
14309918/1      0       N1      34082   60      50M     *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      BBB0AGGGGGGGGG@DGCGGGGGGGGGGGGGGGGGEGGGEFBGGGGFGEE     AS:i:0   XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:50 YT:Z:UU NH:i:1  RG:Z:AD941-1_2_3
18576534/1      256     N1      36329   1       50M     *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      BBCCCEDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG     AS:i:0   ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:50 YT:Z:UU NH:i:2  RG:Z:AD941-1_2_3
3592700/1       272     N1      43888   0       8S42M   *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      GGGGGEGGGGGGGGGGGGGGGGGGGGGDGGGGGGGFGGGGEGGGEBBBBB     AS:i:-8  ZS:i:-8 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:42 YT:Z:UU NH:i:2  RG:Z:AD941-1_2_3
29278996/1      272     N1      43966   1       50M     *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      GGGGGGGGGGGGGGGGGGDGFGGGGGGGGGGGGGGGGGGGGGGFGCCCCC     AS:i:0   ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:50 YT:Z:UU NH:i:2  RG:Z:AD941-1_2_3
36734664/1      272     N1      43967   1       50M     *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      GGGGGGGGGGGFGGGGGGGGBEGGGGGFGGGGGGGGFGGGGGGGGCCCCC     AS:i:0   ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:50 YT:Z:UU NH:i:2  RG:Z:AD941-1_2_3
9698124/1       272     N1      43970   0       46M4S   *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN      GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFE:0BBA     AS:i:-4  ZS:i:-4 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:46 YT:Z:UU NH:i:2  RG:Z:AD941-1_2_3
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