User: sorrymouse

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sorrymouse70
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Posts by sorrymouse

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Comment: A: Antisense transcription from strand specific RNA-seq
... I agree that there is probably a simpler way to do this rather than splitting the files, but it was reassuring to make sure at each step that what should be happening was happening, by checking in IGV. I will say that running stringtie separately on the negative and positive reads increases the num ...
written 10 days ago by sorrymouse70
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Answer: A: Antisense transcription from strand specific RNA-seq
... What I ended up doing is somewhat redundant I think, but its as follows: ##map the reads with hisat2 ./hisat2 --phred33 --rna-strandness RF -x reference.fa -1 reads1.fq -2 reads2.fq -S out.sam ##convert and sort with samtools samtools view -Su out.sam | samtools sort - out.sorted ##fir ...
written 11 days ago by sorrymouse70 • updated 11 days ago by h.mon21k
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Antisense transcription from strand specific RNA-seq
... I have a number of libraries prepared with the Illumina Tru-seq strand specific library prep kit. I want to detect sense and antisense transcription of each gene. I mapped the reads using hisat2 with the --rna-strandedness RF option. The recommendations I can find for separating the bam files by ...
rna-seq written 12 days ago by sorrymouse70
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snpEff database error
... I do not have a problem generally downloading databases from snpEff. I downloaded the mus musculus database just fine using the following command: java -jar snpEff.jar download GRCm38.75 and it is in my 'data' folder: cd data/ ls GRCm38.75 However I need the Drosophila database and when I at ...
database snpeff java written 23 months ago by sorrymouse70
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Answer: A: Variant Calling In Samtools And Freebayes
... Here is the variant I wrote about: chr . A C 999 . . GT:PL:GQ 1/1:255,81,0:78 1/1:255,148,0:99 ./.:0,0,0:3 1/1:255,90,0:87 ./.:0,0,0:3 1/1:119,24,0:21 1/1:255,181,0:99 0/1:255,0,255:99 ./.:0,0,0:3 0/0:0,66,255:63 0/0:0,66,255:63 0/0:0,42,255:3 ...
written 4.7 years ago by sorrymouse70
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Variant Calling In Samtools And Freebayes
... I've used both on the same input files, with essentially default parameters. I am using multiple samples that are supposedly from two populations. freebayes --fasta-reference reference.fa reads.bam > out.vcf samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf ...
samtools written 4.7 years ago by sorrymouse70

Latest awards to sorrymouse

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Antisense transcription from strand specific RNA-seq
Great Question 23 months ago, created a question with more than 5,000 views. For Variant Calling In Samtools And Freebayes
Popular Question 23 months ago, created a question with more than 1,000 views. For snpEff database error
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Variant Calling In Samtools And Freebayes

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