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comprna / SUPPA

SUPPA: Fast quantification of splicing and differential splicing
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Can diffsplice deal with condition only has one sample（no replications） #159

Closed QingCheZhang closed 1 year ago

QingCheZhang commented 1 year ago

Hi I haven't do replications per condition，so every psi and tpm file has only one column.

psi: Col-ck 1:10071000_and_AT1G28660_and_AT1G28670_and_1:10074000;RI:1:10072181:10072457-10072530:10072675:- 0.09523809523809523 1:10071000_and_AT1G28660_and_AT1G28670_and_1:10074000;RI:1:10074993:10075269-10075360:10075508:- 0.47826086956521735 1:10134000_and_AT1G29040;RI:1:10134505:10134536-10134686:10134797:+ 0.1481481481481481 1:10134000_and_AT1G29040;RI:1:10134505:10134581-10134686:10134797:+ 0.039603960396039604 1:10174000_and_AT1G29120;RI:1:10176987:10177042-10177138:10177190:+ NA

tpm: Col-ck 100:1000|3210c02b-6746-4942-a437-25af4e6bd472 1.1198814418846859 100:1002|22dd967b-1149-40ce-b69b-387eb16de2b1 2.9863505116924953 100:1002|46ba8a56-d93b-4911-9fce-d99131fc1c3e 1.4931752558462477 100:1002|d7d36d7b-5a77-4b0b-a366-bc3a60cc36cc 1.1198814418846859 100:1002|f970dbc9-4545-4395-8aec-b1339bd3f082 0.3732938139615619

when i run diffsplice: suppa.py diffSplice --method empirical --input all-suppa_RI_strict.ioe --psi Col-ck-RI-psl.psi Col-heat-RI-psl.psi --tpm Col-ck-all-tpm Col-heat-all-tpm --area 1000 --lower-bound 0.05 -gc -nan 0.7 -o Col-ck-heat

some error occurs: Calculating differential analysis between conditions: Col-ck-RI-psl and Col-heat-RI-psl ERROR:main:Unknown error: (<class 'IndexError'>, IndexError('list index out of range',), <traceback object at 0x7f60a9b64908> I've checked the format of input files and -nan option,as well as --pool-genes options, they don't work, so could it because i don't have replications? Thanks Qing

EduEyras commented 1 year ago

Hi Unfortunately yes, you need replicates

You could try considering deltaPSI vs average TPM and see whether there are high |deltaPSI| at high average expression. Those would be good candidates of differential splicing

E

On Mon, 13 Mar 2023 at 23:37, QingChe Zhang @.***> wrote:

Hi I haven't do replications per condition，so every psi and tpm file has only one column.

psi: Col-ck 1:10071000_and_AT1G28660_and_AT1G28670_and_1:10074000;RI:1:10072181:10072457-10072530:10072675:- 0.09523809523809523 1:10071000_and_AT1G28660_and_AT1G28670_and_1:10074000;RI:1:10074993:10075269-10075360:10075508:- 0.47826086956521735 1:10134000_and_AT1G29040;RI:1:10134505:10134536-10134686:10134797:+ 0.1481481481481481 1:10134000_and_AT1G29040;RI:1:10134505:10134581-10134686:10134797:+ 0.039603960396039604 1:10174000_and_AT1G29120;RI:1:10176987:10177042-10177138:10177190:+ NA

tpm: Col-ck 100:1000|3210c02b-6746-4942-a437-25af4e6bd472 1.1198814418846859 100:1002|22dd967b-1149-40ce-b69b-387eb16de2b1 2.9863505116924953 100:1002|46ba8a56-d93b-4911-9fce-d99131fc1c3e 1.4931752558462477 100:1002|d7d36d7b-5a77-4b0b-a366-bc3a60cc36cc 1.1198814418846859 100:1002|f970dbc9-4545-4395-8aec-b1339bd3f082 0.3732938139615619

when i run diffsplice: suppa.py diffSplice --method empirical --input all-suppa_RI_strict.ioe --psi Col-ck-RI-psl.psi Col-heat-RI-psl.psi --tpm Col-ck-all-tpm Col-heat-all-tpm --area 1000 --lower-bound 0.05 -gc -nan 0.7 -o Col-ck-heat

some error occurs: Calculating differential analysis between conditions: Col-ck-RI-psl and Col-heat-RI-psl ERROR:main:Unknown error: (<class 'IndexError'>, IndexError('list index out of range',), <traceback object at 0x7f60a9b64908> I've checked the format of input files and -nan option,as well as --pool-genes options, they don't work, so could it because i don't have replications? Thanks Qing

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QingCheZhang commented 1 year ago

Hi Unfortunately yes, you need replicates You could try considering deltaPSI vs average TPM and see whether there are high |deltaPSI| at high average expression. Those would be good candidates of differential splicing E On Mon, 13 Mar 2023 at 23:37, QingChe Zhang @.> wrote: Hi I haven't do replications per condition，so every psi and tpm file has only one column. psi: Col-ck 1:10071000_and_AT1G28660_and_AT1G28670_and_1:10074000;RI:1:10072181:10072457-10072530:10072675:- 0.09523809523809523 1:10071000_and_AT1G28660_and_AT1G28670_and_1:10074000;RI:1:10074993:10075269-10075360:10075508:- 0.47826086956521735 1:10134000_and_AT1G29040;RI:1:10134505:10134536-10134686:10134797:+ 0.1481481481481481 1:10134000_and_AT1G29040;RI:1:10134505:10134581-10134686:10134797:+ 0.039603960396039604 1:10174000_and_AT1G29120;RI:1:10176987:10177042-10177138:10177190:+ NA tpm: Col-ck 100:1000|3210c02b-6746-4942-a437-25af4e6bd472 1.1198814418846859 100:1002|22dd967b-1149-40ce-b69b-387eb16de2b1 2.9863505116924953 100:1002|46ba8a56-d93b-4911-9fce-d99131fc1c3e 1.4931752558462477 100:1002|d7d36d7b-5a77-4b0b-a366-bc3a60cc36cc 1.1198814418846859 100:1002|f970dbc9-4545-4395-8aec-b1339bd3f082 0.3732938139615619 when i run diffsplice: suppa.py diffSplice --method empirical --input all-suppa_RI_strict.ioe --psi Col-ck-RI-psl.psi Col-heat-RI-psl.psi --tpm Col-ck-all-tpm Col-heat-all-tpm --area 1000 --lower-bound 0.05 -gc -nan 0.7 -o Col-ck-heat some error occurs: Calculating differential analysis between conditions: Col-ck-RI-psl and Col-heat-RI-psl ERROR:main:Unknown error: (<class 'IndexError'>, IndexError('list index out of range',), <traceback object at 0x7f60a9b64908> I've checked the format of input files and -nan option,as well as --pool-genes options, they don't work, so could it because i don't have replications? Thanks Qing — Reply to this email directly, view it on GitHub <#159>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB23S67I657THSHHZQLW37RXJANCNFSM6AAAAAAVZ4TDF4 . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks for your quick reply, I really appreciate that. Buy the way, what does "average TPM" mean. Is it average TPM of a transcript, or the average TPM of a sample? Thanks in advance