User: bioguy24

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bioguy24190
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Chicago
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Posts by bioguy24

<prev • 220 results • page 1 of 22 • next >
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Comment: C: prepare file for depth of coverage
... input file (getRefegene.txt) #bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames 0 NM_001308203.1 chr1 + 66999251 67216822 67000041 67208778 22 66999251,66999928,67091529,67098752,67105459,67108492,67109226,671366 ...
written 11 weeks ago by bioguy24190
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prepare file for depth of coverage
... Trying to prepare a Rod file for use with GATK depth of coverage. I downloaded a standard hg1g refseq file and I need to remove non-standars contigs other then chr1-22 chrx and y and chrM and sort in karotypic order. Is the below the best way to do so? Thank you :). cat getRefGene.txt | grep - ...
depth of coverage written 11 weeks ago by bioguy24190
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targets in a bed at or above a coverage
... Is there a tool that will calculate percentage of targets in a bed file at or above 250x reads from a bam file? Currently I use bedtools to get all the reads that map to a target, followed by awk to calculate percentage above 250. However, since now our sequencing has increased there may be a more ...
bedfile bam 250x written 4 months ago by bioguy24190 • updated 4 months ago by harold.smith.tarheel4.5k
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STAR-Fusion error while executing and produces some intermediates files
... I have run STAR and am now executing STAR-Fusion on the Chimeric.out.Junction.Out and it executes but I get the below error and no output is produced. I am not sure what the error means, am I missing something? Thank you :). **version** STAR-2.7.0f STAR-Fusion 1.6.0 **command** ST ...
star-fusion written 5 months ago by bioguy24190
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Comment: C: report every base in a bam using bed as input
... Thank you very much :). ...
written 6 months ago by bioguy24190
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report every base in a bam using bed as input
... Trying to output all lines (variant or reference) in the bed file using the below command. Most are SNP's but not all. The command does execute and produce the current output which is ok but why is it only 1 line from the bed? Is there a better approach? Using Samtools and Bcftools 1.9. Thank you :) ...
samtools bcftools written 6 months ago by bioguy24190 • updated 6 months ago by Pierre Lindenbaum124k
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Answer: A: compare two columns of two files
... Another awk: awk 'NR==FNR{c[$2]++;next};c[$1] > 0' file1 file2 ...
written 6 months ago by bioguy24190
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Comment: C: correct mark duplicated error using python and pysam to filter out secondary ali
... I have re-mapped and markduplicates seems ok but I am curious if the python script is close? Thank you :). ...
written 6 months ago by bioguy24190
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Answer: A: Extract gene names from annotated vcf file
... I have not used SNPeff, but if the gene name is always in the fourth field seperated by | awk -F'|' '{print $4}' ...
written 6 months ago by bioguy24190
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correct mark duplicated error using python and pysam to filter out secondary alignments
... I am new to python and trying to learn. The below is an attempt to filter out secondary reads in a all bam files in a directory using pysam. I ran mark duplicates and got an error on several bam files due to secondary alignments. I added comments to each line to illustrate my thought process. I thin ...
python pysam written 6 months ago by bioguy24190

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