Dear all ,
I tried to use eXpress to count the mapping results obtained with Bowtie2.
The command used is
express -m 450 -s 100 --no-update-check transcriptome.fasta MT121_3_sorted.bam
however I obtain the following error message when I used a BAM file as input:
2016-Oct-21 23:34:59 - Attempting to read 'MT121_3_sorted.bam' in BAM format...
2016-Oct-21 23:34:59 - Input is not in BAM format. Trying SAM...
2016-Oct-21 23:34:59 - SEVERE: Unable to open input SAM file '/MT100_3.sam'.
and this one if I use a SAM file as input
2016-Oct-24 21:01:27 - SEVERE: Unable to open input SAM file '/MT121_3_sorted.sam'.
2016-Oct-24 21:01:27 - Attempting to read '/MT121_3_sorted.sam' in BAM format...
2016-Oct-24 21:01:27 - Input is not in BAM format. Trying SAM...
The sam look like a reel SAM :
@HD VN:1.0 SO:coordinate
@SQ SN:c1_g1_i1 LN:241
@SQ SN:c1_g2_i1 LN:279
@SQ SN:c2_g1_i1 LN:319
@SQ SN:c2_g2_i1 LN:222
@SQ SN:c3_g1_i1 LN:642
@SQ SN:c4_g1_i1 LN:323
@SQ SN:c5_g1_i1 LN:234
@SQ SN:c6_g1_i1 LN:396
@SQ SN:c6_g2_i1 LN:351
@SQ SN:c8_g1_i1 LN:334
@SQ SN:c9_g1_i1 LN:214
@SQ SN:c10_g1_i1 LN:300
@SQ SN:c11_g1_i1 LN:432
@SQ SN:c12_g1_i1 LN:254
@SQ SN:c13_g1_i1 LN:282
@SQ SN:c15_g1_i1 LN:563
......
@SQ SN:c79885_g1_i1 LN:204
@SQ SN:c79886_g1_i1 LN:243
@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
...
HWI-ST909:410:C8P7RACXX:6:1203:6648:51518 147 c1_g2_i1 136 40 100M = 100 -136 ACTCTGATATTCTCTGCATCCACTGTAAATGTTCATCATTGGCACATGTT
CCCGCAGAATTGCTGGGGCCTCTTTTGTGTCTGTATGGATCCAAATTAAT <FFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFIIFFIIIIIIIIIIIFIIIIFIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB AS:i:-10 XN:i:0 XM:i:285XO:i:01 XG:i:0 NM:i:2 MD:Z:9C84G5 YS:i:-18 YT:Z:CP
HWI-ST909:410:C8P7RACXX:6:1304:8532:81357 147 c1_g2_i1 144 42 100M = 24 -220 ATTCTCTGCATCCACTGTAAATGTTCATCATTGGCACATGTTCCCGCAGA
ATTGCTGGGGCCTCTTTTGTGTCTGTATGGATCCAAATTAATATGTTCTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB AS:i:-11 XN:i:0 XM:i:286XO:i:01 XG:i:0 NM:i:2 MD:Z:1C84G13 YS:i:-11 YT:Z:CP
HWI-ST909:410:C8P7RACXX:6:2106:12948:92662 99 c4_g1_i1 53 42 100M = 100 147 GTCAGACTTAGACGATGAGTACCTGAGATTATTTTTGTAGTATTTGATGT
CAGATCCACCTCTGACCCAGCCAATCTTCTTCTGCTGAGCATTTTTCTCA BBBFFFFFFFFFFIIIIIIFIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFB AS:i:-6 XN
:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:72G27 YS:i:-6 YT:Z:CP
HWI-ST909:410:C8P7RACXX:6:2211:7081:59369 69 c4_g1_i1 69 0 * = 69 0 GGTAGTCCTGTAAATCTGTGTAAGTATAGGGATAACAATGTGCAAAGTAG
ACTGTATCGTTATNGTGCTGGAAATCTACAGTCCACGTTAGGGAGTAGAA BBBFFFFFFFFFFIIIIIIFIFIIIIIIIIIIIIIIIIIIFIIIFIIFIIIIIIFFIIIFIII#0<FFIIIIIIIFIIFFFFFFFFFFFFFFFFFBBFBF YT:Z:UP
HWI-ST909:410:C8P7RACXX:6:2211:7081:59369 153 c4_g1_i1 69 42 100M = 69 0 GAGTACCTGAGATTATTTTTGTAGTATTTGATGTCAGATCCACCTCTGAC
CCAGCCAATCTTCTTCTGCTGAGCATTTTTCTCACTGTACACCAGAGGCC FFFBBBBFFFFFFFFFFFFFFFFFFFFFFFFIIIFIIIIIFBIIIIIFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFIIIFFFFFFFFFFBBB AS:i:-6 XN
:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:56G43 YT:Z:UP
HWI-ST909:410:C8P7RACXX:6:2106:12948:92662 147 c4_g1_i1 100 42 100M = 53 -147 TGTCAGATCCACCTCTGACCCAGCCAATCTTCTTCTGCTGAGCATTTTTC
TCACTGTACACCAGAGGCCTCATTCCACAGTTATATAAACTGTCAGGCTT BFFFFFBBFBBFFFFFFFFFFFFFFIIIIIIIFIIIIIIIIIIIIIIIFFIIIIIIIIFFIIIIIIIIIIIIIIIIFIIIIIIIIIIFFFFFFFFFFBBB AS:i:-6 XN
:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:25G74 YS:i:-6 YT:Z:CP
Does anyone have an idea to solve this problem ?
Best regards,
Jeremie
I tried to use eXpress to count the mapping results obtained with Bowtie2.
The command used is
express -m 450 -s 100 --no-update-check transcriptome.fasta MT121_3_sorted.bam
however I obtain the following error message when I used a BAM file as input:
2016-Oct-21 23:34:59 - Attempting to read 'MT121_3_sorted.bam' in BAM format...
2016-Oct-21 23:34:59 - Input is not in BAM format. Trying SAM...
2016-Oct-21 23:34:59 - SEVERE: Unable to open input SAM file '/MT100_3.sam'.
and this one if I use a SAM file as input
2016-Oct-24 21:01:27 - SEVERE: Unable to open input SAM file '/MT121_3_sorted.sam'.
2016-Oct-24 21:01:27 - Attempting to read '/MT121_3_sorted.sam' in BAM format...
2016-Oct-24 21:01:27 - Input is not in BAM format. Trying SAM...
The sam look like a reel SAM :
@HD VN:1.0 SO:coordinate
@SQ SN:c1_g1_i1 LN:241
@SQ SN:c1_g2_i1 LN:279
@SQ SN:c2_g1_i1 LN:319
@SQ SN:c2_g2_i1 LN:222
@SQ SN:c3_g1_i1 LN:642
@SQ SN:c4_g1_i1 LN:323
@SQ SN:c5_g1_i1 LN:234
@SQ SN:c6_g1_i1 LN:396
@SQ SN:c6_g2_i1 LN:351
@SQ SN:c8_g1_i1 LN:334
@SQ SN:c9_g1_i1 LN:214
@SQ SN:c10_g1_i1 LN:300
@SQ SN:c11_g1_i1 LN:432
@SQ SN:c12_g1_i1 LN:254
@SQ SN:c13_g1_i1 LN:282
@SQ SN:c15_g1_i1 LN:563
......
@SQ SN:c79885_g1_i1 LN:204
@SQ SN:c79886_g1_i1 LN:243
@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
...
HWI-ST909:410:C8P7RACXX:6:1203:6648:51518 147 c1_g2_i1 136 40 100M = 100 -136 ACTCTGATATTCTCTGCATCCACTGTAAATGTTCATCATTGGCACATGTT
CCCGCAGAATTGCTGGGGCCTCTTTTGTGTCTGTATGGATCCAAATTAAT <FFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFIIFFIIIIIIIIIIIFIIIIFIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB AS:i:-10 XN:i:0 XM:i:285XO:i:01 XG:i:0 NM:i:2 MD:Z:9C84G5 YS:i:-18 YT:Z:CP
HWI-ST909:410:C8P7RACXX:6:1304:8532:81357 147 c1_g2_i1 144 42 100M = 24 -220 ATTCTCTGCATCCACTGTAAATGTTCATCATTGGCACATGTTCCCGCAGA
ATTGCTGGGGCCTCTTTTGTGTCTGTATGGATCCAAATTAATATGTTCTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB AS:i:-11 XN:i:0 XM:i:286XO:i:01 XG:i:0 NM:i:2 MD:Z:1C84G13 YS:i:-11 YT:Z:CP
HWI-ST909:410:C8P7RACXX:6:2106:12948:92662 99 c4_g1_i1 53 42 100M = 100 147 GTCAGACTTAGACGATGAGTACCTGAGATTATTTTTGTAGTATTTGATGT
CAGATCCACCTCTGACCCAGCCAATCTTCTTCTGCTGAGCATTTTTCTCA BBBFFFFFFFFFFIIIIIIFIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFB AS:i:-6 XN
:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:72G27 YS:i:-6 YT:Z:CP
HWI-ST909:410:C8P7RACXX:6:2211:7081:59369 69 c4_g1_i1 69 0 * = 69 0 GGTAGTCCTGTAAATCTGTGTAAGTATAGGGATAACAATGTGCAAAGTAG
ACTGTATCGTTATNGTGCTGGAAATCTACAGTCCACGTTAGGGAGTAGAA BBBFFFFFFFFFFIIIIIIFIFIIIIIIIIIIIIIIIIIIFIIIFIIFIIIIIIFFIIIFIII#0<FFIIIIIIIFIIFFFFFFFFFFFFFFFFFBBFBF YT:Z:UP
HWI-ST909:410:C8P7RACXX:6:2211:7081:59369 153 c4_g1_i1 69 42 100M = 69 0 GAGTACCTGAGATTATTTTTGTAGTATTTGATGTCAGATCCACCTCTGAC
CCAGCCAATCTTCTTCTGCTGAGCATTTTTCTCACTGTACACCAGAGGCC FFFBBBBFFFFFFFFFFFFFFFFFFFFFFFFIIIFIIIIIFBIIIIIFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFIIIFFFFFFFFFFBBB AS:i:-6 XN
:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:56G43 YT:Z:UP
HWI-ST909:410:C8P7RACXX:6:2106:12948:92662 147 c4_g1_i1 100 42 100M = 53 -147 TGTCAGATCCACCTCTGACCCAGCCAATCTTCTTCTGCTGAGCATTTTTC
TCACTGTACACCAGAGGCCTCATTCCACAGTTATATAAACTGTCAGGCTT BFFFFFBBFBBFFFFFFFFFFFFFFIIIIIIIFIIIIIIIIIIIIIIIFFIIIIIIIIFFIIIIIIIIIIIIIIIIFIIIIIIIIIIFFFFFFFFFFBBB AS:i:-6 XN
:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:25G74 YS:i:-6 YT:Z:CP
Does anyone have an idea to solve this problem ?
Best regards,
Jeremie
