cxzhu / simple-seq Goto Github PK

Dear authors:

I am currently using the SIMPLE-seq preprocessing pipeline available on GitHub to process the data mentioned in the article, GSE197740 (mESC_SIMPLE, PBMC_SIMPLE, and mouse_brain_SIMPLE). However, this preprocessing pipeline is only applicable for processing paired-end sequencing data. Therefore, I have only processed GSM7291623 (mouse_brain_SIMPLE). It would be great if you could provide a workflow for processing SIMPLE-seq single-end data.

While processing the GSM7291623 (mouse_brain_SIMPLE) data, I encountered some issues. It would be great if you could help me resolve them. During the mapping to the genome step, while using Bowtie2 for alignment, I encountered the following error:
"Error:ReadSRR24423085.6972:AAATTGCTAG:TTAATACAACTATGTGGTCCAGCGGCCACTATCCCACTCCTATCCAAGGTCGAGGGCCAACATTAGGAAGGCTGCCGCCACCACTGTGAGGGCGCCTGACCATGACCACTGCTTTAGAACAAATGGAAGCACTTGTTTGCAAATTGTCCG:F:,,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:45:72:04 has more quality values than read characters." Later, I located this particular read and examined it, as shown in the following figure.

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With a trial-and-error mindset, I replaced symbols with corresponding letters in the second or third line, and the script ran successfully. However, during the step "zcat SRR24423085_mapped.sam.gz | samtools sort - -o SRR24423085_mapped_sorted.bam", I encountered the following error: "query name too long," as shown in the figure below.

I have downloaded and aligned the samples from the nature paper using this pipeline, but I have the impression that around %20 of the runtime is spent on (de)compression of the raw/intermediatery files.
Given that, most of the HPC environments have relatively slow I/O operations, it could be better to just work with uncompressed files directly.

In here

and here

you are missing a "\t" after $bc.