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Bharati,Originally posted by bharati View Post
Is the sam2mrf command in your $PATH? If not, you need to provide full directory path to that command when you try to run that command.
If this does not address the "error" you got then please provide the exact error message you are getting.Code:sort -r file.sam | /path_to_this_file/sam2mrf > file.mrf
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I am unable to use sam2mrf of RSEQtools, can anybody pls help?
The command I tried was "sort -r file.sam | sam2mrf > file.mrf"
as specified in the manual for the alignment file generated by tophat but it didnt work.
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RSeqtools, bed2interval conversion
Greetings,
Has anyone worked with the utility in RSeqtools that converts .bed format to interval? I have tried it and find that strand information is missing from my output file. See example below:
BED_1 chr20 . 123292 126094 1 123292 126094
BED_2 chr20 . 251843 256677 1 251843 256677
BED_3 chr20 . 256662 257502 1 256662 257502
BED_4 chr20 . 257721 257933 1 257721 257933
BED_5 chr20 . 257954 259040 1 257954 259040
Any advice on what's going on here would be greatly appreciated!
Many thanks!
labrat73
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Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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