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Recent Replies
Comment: Interpreting the meaning of outward facing reads
by
jsuzuki
▴
10
i am back to being confused.
I looked on IGV and grouped reads by read pair orientation. There, i could see all the outward facing reads ga…
Comment: Plotting Correlation matrix
by
Zhiyi
▴
10
It seems in this package the size of the square corresponds to the correlation coefficient instead of the pvalue. Is there a way to make la…
Comment: merging and annotating bcf files for variant calling
by
pr.khavari
•
0
WARNING: Environment variable LD_PRELOAD already has value [], will not forward new value [/usr/local/xalt/xalt/lib64/libxalt_init.so] from…
Comment: Cut & run - bowtie2 dovetail option
by
baijiangshan9726
•
0
Hi, I am just wondering where you found those statements "Dovetail alignment policy. Bowtie210 aligns each mate of a pair separately and th…
Comment: extracting input files form Seurat
by
GenoMax
125k
Just to be clear, you want to export the (input) data used for plots into actual files?
Comment: Error while using rpy2
by
sidrah.maryam
▴
40
Thanks for your comment.
The code that causes this is :
%%R -i adata_test -o ent_de -o paneth_de
#Convert SingleCellExperim…
Comment: Reads are marked as full of mismatches in IGV, but cigar string shows full lengt
by
jsuzuki
▴
10
Very helpful addition, thank you both!
Comment: Downloading 450k methylation data from GEO
by
GenoMax
125k
If you need to download the IDAT files then you can simply get the entire archive using: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE…
Comment: Practical Haplotype Graph Consensus and Imputation Specifications
by
tkosfeld
•
0
The accuracy of seq_len and the database as a whole has been excellent, we trust your math for sure!
I think our concern is little more ab…
Comment: Reads are marked as full of mismatches in IGV, but cigar string shows full lengt
by
LChart
1.8k
To piggyback: "M" in the cigar string indicates an **alignment** match. You can look at the "NM:" tag for the number of mismatches which, i…
Answer: Reads are marked as full of mismatches in IGV, but cigar string shows full lengt
by
swbarnes2
13k
CIGAR strings do not indicate SNPs, only indels and clipping.
Comment: How do I remove certain reads from my raw sequencing data using BLAST?
by
GenoMax
125k
`bbduk.sh` in filter mode (which is the default). You will need to provide a set of sequences you want to check against.
If you want to c…
Answer: CNVkit error "pysam.utils.SamtoolsError: "samtools returned with error 2: stdout
by
ATpoint
68k
> fail to open index BAM file
This suggests that an index is required but missing. Be sure that the bam file is sorted by position with …
Comment: CNVkit error "pysam.utils.SamtoolsError: "samtools returned with error 2: stdout
by
Giuseppe
•
0
Hi @bgilijia3
How have you resolved the problem?
Thank you
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