Hello All!
I am new to coding. I have written a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess...
13 results in 0.0044 seconds.
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Help with sorting sam files in python!
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Sorting Amino Acid Sequences
I have a a set of three fasta files with amino acid sequences. Can you suggest me scripts to separate out sequences that are common, and as well that...Last edited by satishg; 08-25-2015, 11:39 AM. -
Can't sort BAM file ("not a BAM file")
Dear everyone,
I try to convert some SAM files to BAM files following the Samtools FAQ method :
First indexing my reference fasta... -
Sort bed file by chr order and not lexicographically
I've been trying to sort a bed file with bedtools and bedops.
Both seem to sort the bed file lexicographically.
That means if... -
a general question on DEXSeq data preparations
I was following the steps in the vignette of DEXSeq here to construct the exon count files (.txt) for each of my 16 biological samples. However, as shown... -
Smatools mpileup thinks my sorted bam files are not sorted
Hi
I am trying to run samtools mpileup on a large list of bam files
...Code:samtools mpileup -d 5000 -f /path/to/ref.fa \ /path/to/first.bam
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Sorting BAM by chromosome produces a much larger file.
Hi,
I am working with BAM files and I need to sort them.
I've realized that sorting by chromosome produces a file that's around...Last edited by aramadhan; 01-18-2013, 11:55 AM. -
SAM/BAM sort by read names produces truncated read names
Hi,
I tried to sort the alignment file by read name, but it appears that truncated read names were produced. This phenomenon was observed... -
different md5sum id for same BAM file
Hi guys:
I am new to sequencing and going to ask some silly questions...
I got some sequence data from the core facility... -
Novosort
Hi,
If you like to try Novosort the download at www.novocraft.com contains a trial license good until 1 September. The latest version includes... -
samtools: "sort by name" and fast random access
I understand that sorting a BAM file, e.g.will allow for faster random access. This makes sense, as viewing...Code:samtools sort my_file.bam my_file.sorted
Last edited by cycomatto; 12-21-2011, 07:44 AM. -
help me on reheader ".bam for indexing and mpileup
I aligned short reads by an nonpublished aligner. Then I converted the alignments to sam, then bam, and sote bam. They worked for me. Now, I intend to... -
Library prep using chromosome sorted DNA
Does anyone have any experience with library preparation of chromosome sorted DNA? The main issue is that we are starting with only 120ng of material....
