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paper statistics

updated 14 months ago by Ram 43k • written 9.4 years ago by mikhail.shugay 3.5k

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journal

updated 11 months ago by Ram 43k • written 6.1 years ago by heref ▴ 20

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next-gen

updated 13 months ago by Ram 43k • written 7.4 years ago by AptRank ▴ 10

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reputation

updated 14 months ago by Ram 43k • written 10.4 years ago by Obi Griffith 20k

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sam bam samtools

updated 11 months ago by Ram 43k • written 3.7 years ago by kojix2 ▴ 250

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biostars bittorrent

updated 15 months ago by Ram 43k • written 9.8 years ago by Istvan Albert 100k

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galaxy sequencing pipeline

updated 13 months ago by Ram 43k • written 8.2 years ago by support ▴ 50

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Popular Question to pramach1 ▴ 40

Recent Replies

Answer: Practical Haplotype Graph v2 not finding correct paths by pjb39 ▴ 200

There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…

Comment: Output file of satools flagstat empty by Mathew ▴ 90

Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…

Comment: Tissue-specific DEG analysis with DEseq2 by BioinfGuru ★ 1.7k

I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…

Comment: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k

> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…

Comment: Output file of satools flagstat empty by GenoMax 142k

If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.

Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100

@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=0,Type=Flag,…

Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100

@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…

Comment: Tophat multiple or unique mapping criteria by Ruqaiya • 0

> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…

Comment: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k

> Still, I can't understand the Invalid tag name: "1000gALT" the following line is missing in the VCF header: ##INFO=<ID=1000gALT,Num…

Answer: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k

INFO at 121387974 is .;CpG this is an invalid INFO column. There is an invalid attribute named '.' followed by the attribute CpG, …

Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100

@Pierre Lindenbaum as I don't know the meaning of `.;` and I've seen there are many in both files, I simply removed them with `grep -v`. …

Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100

My bad I switched positions between the two files when looking the first time. They do indeed look abnormal but how can I fix it? Below the…

Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py by beginner123 • 0

Hi, no I'm using the python implementation as linked above.

Comment: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k

Show us the content of the INFO column at the problematic positions.

Comment: Tissue-specific DEG analysis with DEseq2 by ATpoint 82k

Sounds like full confounding. Be careful. Personally I would not do this comparison. There is no way to distinguish tissue effect from dono…

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