User: shambyross

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shambyross10
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Posts by shambyross

<prev • 29 results • page 1 of 3 • next >
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Answer: A: BED TO BAM INDEXING
... Hi Jen, I just viewed in the UCSC genome browser. Thank you for your help and suggestions. ...
written 3 months ago by shambyross10
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BED TO BAM INDEXING
... Hello I have encountered a problem when trying to create bam index file. The whole purpose of this is to convert .BED file into .BAM to visualize in IGB. bedToBam -i input.bed -g hg19.txt > input.bam samtools index ***_Specific_Peaks.bam ***_Specific_Peaks.bai [E::hts_idx_push] chromosome blo ...
bam written 3 months ago by shambyross10
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Synthetic Sequencing DataSet: Definition
... Hello, I have searched on internet the definition and purpose of synthetic DNA database but cannot find the answer. Can someone explain why someone would like to generate it and how can it be used? Thank you, Ross ...
general written 10 months ago by shambyross10 • updated 10 months ago by Devon Ryan1.8k
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Comment: C: BBMap NoClass Error
... sorry, Jen - next time will go to Java forum. Can I ask questions relevant to bioinformatics tools here - not necessarily galaxy? ...
written 10 months ago by shambyross10
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BBMap NoClass Error
... Hello. I am running the following (see below) in mac terminal as indicated by biostar handbook for proper BBMap installation. Then, I get the error lang.NoClassDefFoundError: in=reads/fq. Can anyone help me to understand and resolve the problem? Thank you, Ross java -Xmx2g -cp /Users/rossshamb ...
bbmap java error dependencies written 10 months ago by shambyross10 • updated 10 months ago by Jennifer Hillman Jackson23k
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Comment: C: Bowtie 2 error
... Devon, the command finally worked. Perhaps it was the -h ...
written 10 months ago by shambyross10
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Comment: C: Bowtie 2 error
... IT also give me the following comment about the wrapper: Command: /Users/rossshamby/src/bowtie2-2.3.0/bowtie2-align-s --wrapper basic-0 -0 (ERR): bowtie2-align exited with value 1 ...
written 10 months ago by shambyross10
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Comment: C: Bowtie 2 error
... Sorry I did actually put in $READ1 ...
written 10 months ago by shambyross10
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Bowtie 2 error
... Hello. I am trying to run bowtie2. This is directly from the Biostarhanbook. Get reference: ACC-JQ340389 efetch -db=nuccore -format=fasta -id=$ACC >.refs/$ACC.fa $ACC dwgsim -N 10000 $ACC.fa $ACC READ1=$ACC.bwa.read1.fastq READ2=$ACC.bwa.read2.fastq index the reference bowtie2-build $ACC.fa ...
line-command bowtie written 10 months ago by shambyross10 • updated 10 months ago by Jennifer Hillman Jackson23k
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Comment: C: MACS2 run error
... Still get the same error. I have checked and I am indeed running python 2.7.12 Any other suggestions? Thank you, Ross ...
written 12 months ago by shambyross10

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