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Comment: C: I have a list of chromosomes, positions, gene ids, and transcript ids (from a ge
5.7 years ago by claudiadast • 0
1
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3
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I have a list of chromosomes, positions, gene ids, and transcript ids (from a gencode GTF file) - how can I get their corresponding REF and ALT value…
genome gencode
5.7 years ago by claudiadast • 0
4
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Error when running Ensembl VEP: "bigWigToWig does not seem to be in your path"
vep SNP ngs ensembl bigwig
updated 6.0 years ago by 20 • written 6.1 years ago by • 0
0
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1
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3.1k
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Comment: C: Using samtools to assess the number of reads that cover a variant position, as w
6.1 years ago by claudiadast • 0
1
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3
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3.1k
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Using samtools to assess the number of reads that cover a variant position, as well as the ratio of ref/alt among those reads
RNA-Seq bam samtools allele balance mpileup
6.1 years ago by claudiadast • 0
0
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1
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1.4k
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Comment: C: Is there a tool or efficient method of confirming that a FASTQ file and BAM file
6.2 years ago by claudiadast • 0
0
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1
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1.4k
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Comment: C: Is there a tool or efficient method of confirming that a FASTQ file and BAM file
6.2 years ago by claudiadast • 0
2
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8
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1.4k
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Is there a tool or efficient method of confirming that a FASTQ file and BAM file contain the same reads?
genome alignment
updated 6.2 years ago by 147k • written 6.2 years ago by • 0
0
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1
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1.4k
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Comment: C: Getting "Mismatch between read length and quals length" error in SortSam.
6.2 years ago by claudiadast • 0
2
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3
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1.4k
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Getting "Mismatch between read length and quals length" error in SortSam.
genome picard sortsam
6.2 years ago by claudiadast • 0
2
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5
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1.9k
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SortSam is failing due to Error Parsing SAM file: ("Tag of type i should have signed decimal value")
genome sort sam sam picard
updated 6.3 years ago by 164k • written 6.3 years ago by • 0
0
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0
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1.9k
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Comment: C: SortSam is failing due to Error Parsing SAM file: ("Tag of type i should have si
6.3 years ago by claudiadast • 0
0
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0
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1.6k
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How to obtain the combined callable regions BED file via BCBio variant-calling pipeline?
bcbio next-gen
6.8 years ago by claudiadast • 0
0
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1
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3.3k
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Getting samtools cram-to-bam error: [E::cram_get_ref] Failed to populate reference for id?
samtools genome bams crams
6.8 years ago by claudiadast • 0
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