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Hi,
I am interested in assessing differential splicing between two populations.
I got PE-50 stranded mRNA libraries, which were mapped with STAR, and I thought on using the output bam files to run…
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Hi,
I have scSLAM-seq from two samples (control, treated). I have aligned the fastq file using STAR Solo and now trying to generate the CIT file from the Bam files. I will next use the CIT in GRAN…
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Hi, I am trying to use rmats2sashimiplot using the bam files but I am getting this error can you please tell me what I am doing wrong ?
Thanks in advance
`(base) raghdakailany@raghdas-air rmat…
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Hi Nicolas,
could you add a function for simple counting of the number of reads. Due to the use of multithreading during duplication marking (using elprep), my bam file doesn't have the same md5sum…
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Hello,
first of all thanks for this really useful tool! I have one BAM file with single nuclei data from 8 conditions. I run the isoquant like this:
isoquant.py --reference /path/Mus_musculus.GRCm3…
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Hi,
I was trying to process a bam file coming from a scATAC sequencing, but after waiting for hours the process seems to be stuck at the beginning (see image attached). The input bam file is 33 Gb …
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I've encountered an issue where Monopogen appears to process multiple samples as a single sample during germline SNV calling, despite correctly handling them as separate samples in the preprocessing s…
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Hi,
I have tcr fastq datasets, and the barcode+umi is 20bp (NCCCAAGGGT+AAAGGTAGTA) instead of the usual 26bp. I wondered if Trust4 could work successfully in this scenario?
Another question is: …
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Hi, I am really appreciated your works. I find only peak files can be download now. Can bigwig or bam files be download? Thank advances!
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Hi,
I'm having trouble finding SNPs overlapping with reads using BAM files generated with BD Rhapsody pipeline. I specified UMI tag (MA) manually and cell barcode is the same (CB). However, the cou…