User: sarajeanne08

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sarajeanne0810
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Posts by sarajeanne08

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Comment: C: STAR RNA - Generate Wiggle Plots from already aligned BAM files
... Hi Devon, Thank you so much for the Deeptools recommendation! It works so well and is easy. Thanks again! ...
written 8 months ago by sarajeanne0810
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Comment: C: STAR RNA - Generate Wiggle Plots from already aligned BAM files
... Hi Icscs, Thank you for your help. I tried running those commands but ended up with a bug: $ STAR --runMode inputAlignmentsFromBAM --inputBAMfile Aligned.sorted.out.trimmed.bam.dupesmarked.bam --outWigType bedGraph --outWigStrand Stranded Feb 07 11:15:48 ..... Reading from BAM, output wiggle BUG: ...
written 8 months ago by sarajeanne0810
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Comment: C: STAR RNA - Generate Wiggle Plots from already aligned BAM files
... Hi Devon, Thank you so much! I really appreciate your help and suggestion. Sara ...
written 8 months ago by sarajeanne0810
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Comment: C: STAR RNA - Generate Wiggle Plots from already aligned BAM files
... I tried to do this but my phone I guess messed up... I will delete it for now until I can fix it ...
written 8 months ago by sarajeanne0810
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Answer: A: STAR RNA - Generate Wiggle Plots from already aligned BAM files
... Do you know if Deeptools can handle paired end reads and strandedness? as I know Bedtools can't handle these properly. Thank you! ...
written 8 months ago by sarajeanne0810
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STAR RNA - Generate Wiggle Plots from already aligned BAM files
... Hi All, Is it possible to re-run STAR RNA aligner to obtain wiggle plots on already aligned and sorted BAM files? Or do I need to re-align again to obtain this type of output? I really do not want to have to re-align - so I am open to other options. Thank you! ...
rna-seq written 8 months ago by sarajeanne0810 • updated 8 months ago by lcscs1234510
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QIIME - Illumina MiSeq, Paired-end Data - Mapping file and Data Preprocessing Questions
... Hi All, I am struggling to pre-process my 16S rRNA gene amplicon Illumina Sequencing data using QIIME. I have several issues that I can't find clear answers for on QIIME's website. I have 4 files from the sequencing - read 1, read 2, index 1 and index 2 (MiSeq Paired End - 2x 250 cycle). V1-V2 re ...
illumina 16s qiime written 10 months ago by sarajeanne0810 • updated 4 months ago by bioxujintian0
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OmicSoft Array Studio V9.0 for DNA-Seq WES Analysis
... Hi All, I am curious if anyone has experience using OmicSoft's Array Studio for WES data analysis. I have BAM files ready to go but I am hoping to learn how their variant calling algorithm (Summarize Mutation Data tool) compares with others like GATK. Thank you very much! ...
variant calling wes written 15 months ago by sarajeanne0810
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Comment: A: Installing VCFTools on CentOS 7
... I tried to run the program but it looks like it may not like my vcf file: --vcf bash: syntax error near unexpected token `newline' I assume this means the format of the file I received is not correct? ...
written 15 months ago by sarajeanne0810
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Answer: A: Installing VCFTools on CentOS 7
... Thank you very much for your help. I was able to continue the installation process after installing zlib-devel. ...
written 15 months ago by sarajeanne0810

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