The below is the BAM file produced by running tophat.
samtools view -h accepted_hits.bam
@HD VN:1.0 SO:coordinate
@SQ SN:Mt:3452:Mt3.5.1Chr1 LN:34297684
@SQ SN:Mt:3453:Mt3.5.1Chr2 LN:34376035
@SQ SN:Mt:3454:Mt3.5Chr3 LN:43359096
@SQ SN:Mt:3455:Mt3.5.1Chr4 LN:47685368
...
...
...
@SQ SN:Mt:3460:AC130806.58 LN:141498
@SQ SN:Mt:3461:AC229707.11 LN:3289
@SQ SN:Mt:3462:AC135504.61 LN:132492
...
...
...
@PG ID:TopHat VN:2.0.4 CL:/usr/local/share/tophat-2.0.4.Linux_x86_64/tophat -p 6 -o IR_t1_Mt -G Mt.gff Mt 121108_I7001139_FCD1FBHACXX_L4_GSL_0040.06_1.fq,121108_I7001139_FCD1FBHACXX_L5_GSL_0040.06_1.fq,121108_I7001139_FCD
1FBHACXX_L6_GSL_0040.06_1.fq,121108_I7001139_FCD1FBHACXX_L7_GSL_0040.06_1.fq,121108_I7001139_FCD1FBHACXX_L8_GSL_0040.06_1.fq
FCD1FBHACXX:5:1114:18853:38567#GCCAATA 0 Mt:3452:Mt3.5.1Chr1 150172 50 100M * 0 0 CCCGGGCGCGTATTGCCGAAAAGAAGGTTTAGCTTCAGTTGTGCTACTCTAGACCTGCGGAAGACAGGTGCTGCATGCAAAGGCCTAAGTCCCGCGATGT bbbeeeeegggggi
hhfigiiehdfffaegdfhiihhiiifcgegggeeeeeeddbddaaaYaa`bca__bbcbcbbcccccbaabb_bcdcbaX[aaa[ AS:i:0 X
...
...
...
However, because of too many colons existing between SN and LN, it seems that cufflinks does not work.
So, I think I will have to remove "Mt:3452:" part.
My question is that "Could I use sed command to edit BAM file?"
samtools view -h accepted_hits.bam
@HD VN:1.0 SO:coordinate
@SQ SN:Mt:3452:Mt3.5.1Chr1 LN:34297684
@SQ SN:Mt:3453:Mt3.5.1Chr2 LN:34376035
@SQ SN:Mt:3454:Mt3.5Chr3 LN:43359096
@SQ SN:Mt:3455:Mt3.5.1Chr4 LN:47685368
...
...
...
@SQ SN:Mt:3460:AC130806.58 LN:141498
@SQ SN:Mt:3461:AC229707.11 LN:3289
@SQ SN:Mt:3462:AC135504.61 LN:132492
...
...
...
@PG ID:TopHat VN:2.0.4 CL:/usr/local/share/tophat-2.0.4.Linux_x86_64/tophat -p 6 -o IR_t1_Mt -G Mt.gff Mt 121108_I7001139_FCD1FBHACXX_L4_GSL_0040.06_1.fq,121108_I7001139_FCD1FBHACXX_L5_GSL_0040.06_1.fq,121108_I7001139_FCD
1FBHACXX_L6_GSL_0040.06_1.fq,121108_I7001139_FCD1FBHACXX_L7_GSL_0040.06_1.fq,121108_I7001139_FCD1FBHACXX_L8_GSL_0040.06_1.fq
FCD1FBHACXX:5:1114:18853:38567#GCCAATA 0 Mt:3452:Mt3.5.1Chr1 150172 50 100M * 0 0 CCCGGGCGCGTATTGCCGAAAAGAAGGTTTAGCTTCAGTTGTGCTACTCTAGACCTGCGGAAGACAGGTGCTGCATGCAAAGGCCTAAGTCCCGCGATGT bbbeeeeegggggi
hhfigiiehdfffaegdfhiihhiiifcgegggeeeeeeddbddaaaYaa`bca__bbcbcbbcccccbaabb_bcdcbaX[aaa[ AS:i:0 X
...
...
...
However, because of too many colons existing between SN and LN, it seems that cufflinks does not work.
So, I think I will have to remove "Mt:3452:" part.
My question is that "Could I use sed command to edit BAM file?"
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