Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.
I have a list of cell lines that should be compared against another list of cell lines as pairs. I am trying to find a way in order for me...
Asked on 07/22/2021 by Yousef
1 answerWhat is the best python tool to convert a SDF file to a structured data frame (pandas.DataFrame). Similar to Molconvert from ChemAxon? SDF can have different datafields for each compound...
Asked on 07/21/2021
1 answerI'm trying to read gctx files with cmapPy. This is my code:from cmapPy.pandasGEXpress.parse_gct import parsefrom cmapPy.pandasGEXpress.write_gct import writeparse("C:/Users/User/Desktop/gctx/CAS9_BASELINE_LEVEL3_BING__n10721x10174.gctx")This is the error:(base) C:UsersUserDesktophello>D:/anaconda/python.exe c:/Users/User/Desktop/gctx/readgcxtx.pyTraceback (most recent...
Asked on 07/20/2021 by blue bells
1 answerI am experiencing timeout problems when downloading the NCBI nr preformatted blast database using the update_blastdb script (version 504861). I run the script with the following paramtersupdate_blastdb --decompress --passive...
Asked on 07/19/2021 by C. Zeil
2 answerI'm trying to understand why RPKM is not an appropriate way to normalize for RNA seq (I understand the general idea, but I'd like to gain a deeper understanding). So...
Asked on 07/19/2021
1 answerI'm trying to compare the output of 2 different algorithms of RNA structure prediction(my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is...
Asked on 07/18/2021
1 answerI have assembled poxvirus genome using Ray. The assembly is good. Out of several thousand contigs I got, I was able to get one scaffold using Contiguator tool, which is...
Asked on 07/17/2021
1 answerI am setting up a HiChIPseq pipeline, but installing software necessary for the HiC side of things has been unbecoming. Both my PI and I have tried to install Hi-C...
Asked on 07/16/2021
2 answerI am trying to establish pipeline in snakePipes and while running DNA mapping I got next IndexError error.(snakePipes) ~ $ DNA-mapping -i /Volumes/HD2/snakePipes_CHIP/ChiPseq -o /Volumes/HD2/snakePipes_CHIP/ChiPseq1 --mapq 5 -j 10...
Asked on 07/15/2021 by Vitaly
0 answerI have a fasta file that contains sequence reads and sequence id file that needed to be removed from the fasta file. I have done this earlier, but since id...
Asked on 07/15/2021
2 answerGet help from others!
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