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Using Coverage Python cript: Run into ValueError

python subprocess coverage written 4.6 years ago by quachtina96 • 40 • updated 4.6 years ago by RamRS ♦ 25k

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prevent [samopen] from being printed by samtools

alignment subprocess samtools written 4.9 years ago by shuelga • 20 • updated 4.9 years ago by Devon Ryan ♦ 93k

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Recent Replies

C: How to extract the list of genes from TCGA CNV data by Kevin Blighe ♦ 53k
You should use my code as a guide to help you through this analysis, but please make modification...
A: Studying for a Bioinformatics degree by Charles Warden ♦ 7.5k
While not a perfect solution, I have some notes on on-line courses here: http://cdwscience.blogs...
C: bbsplit not using all reads in library by ghd1998 • 0
Thanks for your reply! Ambiguous reads are just assigned to the first best site so I don't think ...
C: How to extract the list of genes from TCGA CNV data by A • 3.7k
@Kevin When I try to keep my sample names with my seg file like below sample chr start end ...
C: changing ID in an existing GFF3 file by Ric • 290
I understand, but would it be less confusing if numbered by feature type would be dependent?
C: software of single-cell RNA-seq from fastq or fasta by yueli7 • 100
Thanks, genomax, I will add to that.
C: Fimo and PSSM by Asaf ♦ 6.8k
It's pretty easy to parse the text files, the tsv might even be the PWM. I did this a while ago
A: How to generate CpG REGIONs file to run DMR analysis with methylkit? by Charles Warden ♦ 7.5k
If this is human, perhaps you can consider the UCSC CpG Islands (and you can get some gene mappin...
C: software of single-cell RNA-seq from fastq or fasta by genomax ♦ 76k
It would be beneficial to add what **kind** of single-cell data you have? There are a few differe...
C: sequence in bam file looks weird by swbarnes2 ♦ 7.2k
A quality string with lots of G's is high quality, not low quality. What does the region look li...
A: software of single-cell RNA-seq from fastq or fasta by bioinformatics2020 • 30
I'm a little confused by your question. So you're looking for software that will take your raw si...
A: software of single-cell RNA-seq from fastq or fasta by swbarnes2 ♦ 7.2k
10XGenomics cellranger will take fastqs as input and output files that Seurat can take. But then...

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