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Comment: Filtered reads from assembly and raw reads?

Comment: Multi-allelic sites in Identity-by-descent tract detection

A: How to find the mean inter-marker distance between SNPs from a vcf file?

Comment: resolving specific clusters from data (spectral clustering)

Answer: How to split a long protein sequence in small sequences with same header?

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Comment: Finding the read ratio of transcription termination data using R by margo ▴ 20

Thank you for getting back to me. I have converted my bedgraph file to a dataframe. I am wanting to write a code which applies the function…

Answer: Supplementary alignments in BAM-file by Carlo Yague 8.1k

In one step, you could remove every alignments with a mapping quality of 0. With most aligners, this corresponds to the reads for which the…

Answer: Finding the read ratio of transcription termination data using R by Trivas ▴ 420

Please do not use bedgraph files for this type of analysis. I've used bed files and `bedtools coverage` to calculate the coverage within sp…

Comment: BWA-mem - Different alignment numbers to same reference sequence by GenoMax 117k

Likely since OP says > small sequences of around 150bp

Comment: BWA-mem - Different alignment numbers to same reference sequence by GenoMax 117k

May be of interest: https://jeremy9959.net/Blog/TheMEMinBWAMem-fixed/

Answer: Supplementary alignments in BAM-file by swbarnes2 12k

It might take two steps: 1) using samtools to identify the read names which have supplementary alignments, then 2) filter away all lines in…

Comment: BWA-mem - Different alignment numbers to same reference sequence by swbarnes2 12k

Are those 75k reads longer than seq2?

Comment: How to split a long protein sequence in small sequences with same header? by shenwei356 7.3k

seqkit does not work on this case.

Comment: How to split a long protein sequence in small sequences with same header? by cpad0112 21k

if fasta file is as simple as that, you can try following simple code: $ bioawk -c fastx '{print ">"$name; print substr($seq,1,length(…

Comment: Supplementary alignments in BAM-file by GenoMax 117k

Does this address > i want the whole read to be filtered out whenever it contains > supplementary alignments from the bamfile and not on…

Answer: Supplementary alignments in BAM-file by Pierre Lindenbaum 146k

add `-e '![SA]'` to your samtools view command ( http://www.htslib.org/doc/samtools.html#FILTER_EXPRESSIONS )

Comment: Minimum and maximum depth filert - vcftools by Pierre Lindenbaum 146k

vcftools is deprecated use `bcftools -i 'INFODP>1 && INFO/DP<1000'`

Comment: Filtered reads from assembly and raw reads? by GenoMax 117k

> can be used to get reads from a de-novo assembly if I have the raw > reads? If you have an assembly then the individual reads are no lon…

Answer: ESTIMATION OF LEVEL OF CYTOKINES FROM BULK RNAseq by Rafael Soler ▴ 430

Hello Leticia, I don't know much about Cybersort analysis, but you can check genes related to `cytokine activity` GO Term http://www.inf…

Comment: Supplementary alignments in BAM-file by mokbel73 • 0

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