User: kanika.151

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kanika.15180
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Posts by kanika.151

<prev • 69 results • page 1 of 7 • next >
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Comment: C: Alignment in WES
... Yes, I was told that unpaired single read good quality reads might increase the coverage of a variant and increase the coverage of the sample. Therefore, when unpaired fastq file is processed only high quality mapped reads are kept out of it. I just wanted to know if there are others who think this ...
written 16 days ago by kanika.15180
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Comment: C: Alignment in WES
... I do not have an exact figure but not more than 1% ...
written 16 days ago by kanika.15180
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Alignment in WES
... Hi All, I have a weird question. I have been running a WES pipeline which has been made by someone else. And, they decided to use trimmomatic for the adapter trimming step which produces both: > *.paired.fastq.gz and > *.unpaired.fastq.gz And, these files are processed by BWA-MEM one by o ...
trimmomatic exome wes alignment sequencing written 16 days ago by kanika.15180
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Answer: A: featureCounts with pseudobam
... Hi, I have used the 'psuedobam' from Kallisto to see if it gives me similar results or not. I was using the Linux based version of featureCounts and it worked. I speculate it has something to with the fasta file you have used for indexing its similarity with the gtf file you use for counting. I h ...
written 7 months ago by kanika.15180
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Comment: C: Error ecountered while running conifer with demo data set
... Can you share the command that you are using? ...
written 9 months ago by kanika.15180
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Comment: C: Error ecountered while running conifer with demo data set
... hdf5 1.8 can be found at this location: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/ ...
written 9 months ago by kanika.15180
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Comment: C: Error ecountered while running conifer with demo data set
... Apparently, hdf5 1.8 is not supported with pytables 2.4.0 when I try to install pytables with hdf5 1.8 it says not supported. Did you face the same issue? ...
written 9 months ago by kanika.15180
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Answer: A: tables.exceptions.NoSuchNodeError: group ``/`` does not have a child named ``sam
... Hi, Can I ask you the version of PyTables that you have installed for using Conifer? ...
written 9 months ago by kanika.15180
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Comment: C: Error ecountered while running conifer with demo data set
... Hello! I tried your method and it worked for all the chromosomes except 'chr Y' in the sample data set but that is understandable. Note: I had to change the conifer.py and conifer_functions.py making it compatible with PyTables 3.x. Also, I didn't do any changes with the versions of other tools t ...
written 10 months ago by kanika.15180
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Comment: C: 1 base pair to 'x' byte conversion
... Thank you. I had taken read length into consideration as the data is paired-end. I will do as you all have suggested. Thanks again! :) ...
written 10 months ago by kanika.15180

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Scholar 12 months ago, created an answer that has been accepted. For A: Extract Dendrogram Information From Heatmap Generated By Heatmap.2
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