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Number of bisulfite transformed reads are not equal between Reads 1 and 2 #657
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Hi Jonathan, I would say this is the first time in well over a decade that I see anyone using FastA files for alignment. I am wondering how you got hold of FastA files? The typical procedure would involve downloading the data in FastQ format:
You would then determine which type of library it is, and run the data through Trim Galore (FastQ required). Once that is done you would proceed to the mapping step. And just to make sure that the FastA files you have both have the same number of reads could you run the following to count the number of lines?
I should probably stress that I would recommend the FastQ steps described above. Also as a word of warning: |
Hi Mr. Krueger, |
Hi Felix, chr chrUn_KI270448v1 (7992 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performedThe provided filenames for paired-end alignments are /hicanu/canu-scripts/trimmed/SRR10493736_1_val_1.fq.gz and /hicanu/canu-scripts/trimmed/SRR10493736_2_val_2.fq.gz The error says my input file is not in the fastA format. Kindly help me know where i went wrong and what i can do to resolve the issue. |
Your command contains the flag |
Hello Mr. Felix, bismark --non_directional /home/jupyter/epilepsyvar/dataset/ref_genome/ -1 SRR10493735_1_val_1.fq.gz -2 SRR10493735_2_val_2.fq.gz report> Chromosomal sequence could not be extracted for SRR10493735.33103437_33103437_length=150 chrM 1 |
That's all fine, you just have a few reads that align to the very end of the mitochondrium. Just keep going! |
Dear Bismark Author,
I was running my data with the bismark tool and i got the error message below. the version of bismark is: version v0.24.2 and the code i used to run is:
/home/jkalami/.conda/envs/bismark/bin/./bismark --non_directional --parallel 8 -f /media/biodataD/omics_project/bisulphite-dataset/ref -1 SRR10493735_1.fa -2 SRR10493735_2.fa report.txt
ERROR MESSAGE:
Writing a C -> T converted version of the input file SRR10493735_2.fa.temp.2 to SRR10493735_2.fa.temp.2_C_to_T.fa
Writing a G -> A converted version of the input file SRR10493735_2.fa.temp.2 to SRR10493735_2.fa.temp.2_G_to_A.fa
Created C -> T as well as G -> A converted versions of the FastA file SRR10493735_2.fa.temp.6 (49610851 sequences in total)
[FATAL ERROR]: Number of bisulfite transformed reads are not equal between Read 1 (#49602128) and Read 2 (#49610851).
Possible causes: file truncation, or as a result of specifying read pairs that do not belong to each other?! Please re-specify file names! Exiting...
I hope to hear from you soon.
Kind regards
Jonathan.
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