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Hello,
An error appeared when i used ITIS:
CMD: perl -I /home/ITIS /home/ITIS/transform_to_bed.pl -b test_TN.1502117054/test_TN.all_reads_aln_ref_and_te.sort.bam -e test_TN.1502117054/EZ-Tn5.fast…
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How do I prepare the tn5_barcode.txt, what is the content of the file format?
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Hi Dr. Chen,
Thank you for sharing detailed information about the various single-cell sequencing technologies! I’ve been studying the SHARE-seq method and have a question regarding the design of the …
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Instead of splitting files according to Tn5 barcode, add another FASTQ comment containing the barcode sequences. We can the write all the reads to the same file, and map together. Add a subsequent ste…
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Hi,
I followed your workflow and am getting an error during peakcalling.
This is the error I get from macs2:
AssertionError: Right position must be larger than left position, check your BED f…
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Hello,
First, thank you for creating this great documented pipeline.
Second, I have a few questions about the proccess of the data:
1. in the paper it was written that : "Fastq files were then use…
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Does the pipeline apply the standard +4/-5 offsets to aligned reads to account for the precise Tn5 binding site? I have not been able to find this in the documentation or in the code base.
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Hello,
It looks like SELMA has built-in bias score matrices for DNaseI and Tn5, each called by the '-t DATATYPE' flag. Is it possible for the user to generate/use custom bias matrices for other enz…
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Hi,
Could you maybe add an explanation of what exactly the ATACseq mode (-A flag) is doing differently to DNase mode? Also should the input BAMs for ATACseq mode be Tn5 shifted or not?
Thanks
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**Describe the bug**
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**Expected behavior**
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