Picard VS SAMtools (Conversion & Sorting & Indexing & Removal of duplicates & ...)
As the title, what's your first choice to realize different purposes on your SAM/BAM files? Many thanks in advance!
chip-seq
next-gen
• 855 views
•
link
written
by
leileicui_xuan •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Downsampling ATAC-seq BAM files
written by Elise •Hi all, I have two ATAC datasets sequenced on two sequencers with different read depths. I would like to downsample the one with higher read …
-
DESeq2 input file
written by Bioinf_Questions •Hello. I'm trying to analyzing RNA-seq data with DESeq2 to study differencial gene expression. I have SAM and BAM files generated by samtools. How do …
-
Get unique alignment stats from SAM file with a combined genome
written by Viz •As the title states, I have sam/bam files from alignments of our reads against an index built from two fastA genomes concatenated. From these sam …
-
Loop over .sai files coupled with .fastq.gz
written by Bnf83Hi guys, I'm totally new in the field of ChipSeq histon acetylation data analysis. I have to analyse some ChipSeq data. As from many tutorials …
-
IGV error: Error loading SAM header: For sequence 34711, text and binary have different lengths in …
written by EVRHI, I have sam file and I converted into a bam and later sorted it. I also created bam index for the sorted_bam file. When …
-
differential exon usage
written by Lila MHi everybody! I've downloaded different bam files (RNA-seq) that corresponds to tumor. I have the coordinates for exons of interest, and I would like to …
-
Samtools Adding Head reduces file size
written by martijnkelder •Hi all, I'm trying to convert my SAM to BAM files using samtools, to subsequently view them in IGV. When I do samtools faidx reference.fasta …
-
Bam Header Edit
written by Ashutosh PandeyHi, I have around 20 BAM files and each of them have proper bam header including RG ID, Sample, Library, Platform unit, Description and Platform. …
-
Using Samtools On Many Files Recursively In One Go
written by Vikas Bansal<p>Hi,</p> <p>I have around 30 sam files in my different directories -</p> <pre><code> ./sff*/mapping/out.sam </code></pre> <p>So in my current directory there are around 30 directories …
-
Convert Part Of A Bam File To Sam
written by User 9906 •<p>Is it possible to work on a part of a BAM file?</p> <p>Since these files are huge, I want to extract 1MB of the BAM …
Right tool for the right task. For functions that overlap it is personal choice.