Reg. second step

[RPIASRI]

I want to use McSplicer for predicting AS events in my transcriptome dataset. I had taken annotation in gtf format which is generated by stringtie and run the first step and annotation_refined.gtf file is created.

Further I took the bam files generated through samtools sort and index it to create bai file

but when I am running second step of the program ( ./bin/sigcount ), I am getting following error: "Work with given annotation WARNING: Mate could not be found for:"

Kindly help me with the same.

[canzarlab]

This seems to be a warning, not an error. Did you get (non-zero) counts in the .cnt files? Did you provide single or paired-end reads?

[RPIASRI]

No, I didnt get any count in .cnt file. It was totally blank. I provide paired-end reads. Kindly help me

[canzarlab]

I have just added a new binary for running sigcount with paired-end reads: sigcount_pe in folder bin. Please try and let me know if this solved your problems.

[RPIASRI]

I tried this option but is getting same error, whether using sigcount or sigcount_pe Infact, i reinstall it and then executed but the error was there and zero counts in .cnt file. For your reference, I am providing initial few lines of the error, here:

Work with given annotation WARNING: Mate could not be found for: SRR12772292.9157794 369 CM000126.1 195323 1 46M = 195261 0 ACACACTGCGTCTTGGAGTCCGTGCTACAGCTGGCTACAAATCTGT :::,::,FF,,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 ZS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:46 YT:Z:UP NH:i:5 WARNING: Mate could not be found for: SRR12772292.3462499 385 CM000126.1 244808 1 53M1105N4M = 244728 0 CAAGAACTGTGTTCTCAACTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGTGGG FFFF:FFFFFFFFFFFFFFFF:F:FFFFFFFFFFF,FFFFFFFFFF,FFF,,FF,FF AS:i:-3 ZS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:54C2 YT:Z:UP XS:A:+ NH:i:2

[canzarlab]

sorry for these problem. would you be able to share your bam file or a random sample (e.g. 10% of reads) of it?

[alig99]

Hi, Just wondering if this issue was resolved as I have the same issue receiving segmentation fault (core dumped) when running sigcount_pe with paired end reads. Thank you ali

Work with given annotation WARNING: Mate could not be found for: R100400180029:20230620153811:V350160349:2:1087843:2:51:AATACCGT 177 X 111124287 60 148M 17 50185629 0 TGAAGATAAACTGAAGAATAATGAACCACATTCCATGCAAGAGATTTGTGACTATGCAAGAGGAATTTCCAGAGACATGTCTTTAGACACTGAAATGAATCCAGAAAAAAATTTGTTGGGAGTAAGGGATGGTTTGAGGAATTTAGGG EGB5CABBCFCGCDED;E7=/,B:EGBBFCE4DDG8@@GBDC?F>DD>>E'EB?BD@C?1A1&EE)EB+D9DE?>?;$9F8C=@G<HCCBBDE8?C:DAC<>BB8BADBE=B<?G;CAGDDBG>E?EC<CA?>B7$+ADAE<F@0 AS:i:-2 XN:i:0 XM:i:1 XO:i:0 XG:i:0 YT:Z:UP XS:A:+ NH:i:1 MD:Z:68T79 NM:i:1 WARNING: Mate could not be found for: R100400180029:20230620153811:V350160349:4:247001:1:11:GCGAGATC 97 X 111192586 60 33M1682N115M 22 45323385 0 TAAGAACCCTAATATTGTTAATTATTTAGATAGCTACTTGGTGGGTGATGAACTATGGGTAGTCATGGAATACTTGGCTGGTGGCTCTCTGACTGATGTGGTCACAGAGACCTGTATGGATGAAGGACAGATAGCAGCTGTCTGCAGA DF0GDDG?C3FD9E@=1ABEE>3@>CCDE9CD+HCEFBCCFCF951GCAGBEGCFB>?FAFEDCDCDBEEDDGD=FEFD:EBCFF=GCFDFCCCF5A1CGFDFEDE>CG.FFCCC9ACEECH?1B@C<GD4EFGB,EB?D8B>G)EE AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YT:Z:UP XS:A:+ NH:i:1 MD:Z:148 NM:i:0

[israa-alqassem]

Hi, Sorry for the late response. Do you have paired single end reads? Could you share your bam file with me so I can look into this error?

Hi, Just wondering if this issue was resolved as I have the same issue receiving segmentation fault (core dumped) when running sigcount_pe with paired end reads. Thank you ali

Work with given annotation WARNING: Mate could not be found for: R100400180029:20230620153811:V350160349:2:1087843:2:51:AATACCGT 177 X 111124287 60 148M 17 50185629 0 TGAAGATAAACTGAAGAATAATGAACCACATTCCATGCAAGAGATTTGTGACTATGCAAGAGGAATTTCCAGAGACATGTCTTTAGACACTGAAATGAATCCAGAAAAAAATTTGTTGGGAGTAAGGGATGGTTTGAGGAATTTAGGG EGB5CABBCFCGCDED;E7=/,B:EGBBFCE4DDG8@@gbdC?F>DD>>E'EB?BD@C?1A1&EE)EB+D9DE?>?;$9F8C=@g<HCCBBDE8?C:DAC<>BB8BADBE=BE?ECB7$+ADAE<F@0 AS:i:-2 XN:i:0 XM:i:1 XO:i:0 XG:i:0 YT:Z:UP XS:A:+ NH:i:1 MD:Z:68T79 NM:i:1 WARNING: Mate could not be found for: R100400180029:20230620153811:V350160349:4:247001:1:11:GCGAGATC 97 X 111192586 60 33M1682N115M 22 45323385 0 TAAGAACCCTAATATTGTTAATTATTTAGATAGCTACTTGGTGGGTGATGAACTATGGGTAGTCATGGAATACTTGGCTGGTGGCTCTCTGACTGATGTGGTCACAGAGACCTGTATGGATGAAGGACAGATAGCAGCTGTCTGCAGA DF0GDDG?C3FD9E@=1ABEE>3@>CCDE9CD+HCEFBCCFCF951GCAGBEGCFB>?FAFEDCDCDBEEDDGD=FEFD:EBCFF=GCFDFCCCF5A1CGFDFEDE>CG.FFCCC9ACEECH?1B@C<GD4EFGB,EB?D8B>G)EE AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YT:Z:UP XS:A:+ NH:i:1 MD:Z:148 NM:i:0