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Is there no way to bypass the Windows requirement for working with Thermo RAW files

proteomics mass-spectrometry ms/ms written 5 days ago by uki • 20 • updated 4 days ago by harish • 130

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Error: Sieve v.2.2 (Label-free mass spectrometery differential analysis) - Index bounds outside the array

lfq mass-spectrometry thermo - sieve v2.2 lc-ms/ms written 6 weeks ago by Ramaraj K • 0 • updated 5 weeks ago by Biostar ♦♦ 20

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Predict tissue origin by protein expression

protein mass-spectrometry written 3.9 years ago by Vova Naumov • 220 • updated 3.9 years ago by Laurent • 1.6k

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Recent Replies

C: How to run eXpress RNA-seq quantification? by Charles Warden ♦ 5.4k
While I don't exactly suggest doing benchmarking for the sake of benchmarking, I do think it is i...
C: toil stats under-reporting memory usage? by h.mon ♦ 20k
I don't use CWL or Toil, so I really don't know what they report. But bwa mem with the human geno...
C: Galaxy differential expression starting from raw FASTQ files by english.server • 40
Thanks for your suggestions.
C: motif search with ATACseq by Charles Warden ♦ 5.4k
It's not uncommon to try removing duplicate reads before peak calling with ATAC-Seq. If you do t...
A: A constant problem with SAM file header by h.mon ♦ 20k
I wonder what you consider what you consider "pretty different". The only difference I can see is...
C: A constant problem with SAM file header by genomax ♦ 57k
You should scroll further down in your own file. At some point you should start seeing the reads....
C: A constant problem with SAM file header by swbarnes2 ♦ 4.2k
I'm not seeing the glaring problem. Your reference has multiple sequences, theirs has one. Your...
C: Plot of 2 replicates by Russ • 380
Oh - sorry, I misunderstood. Check out the `separate` command in tidyr, it's specifically designe...
C: Plot of 2 replicates by Friederike • 2.3k
Can you share the code (including the `gather` command) and plot that you generated and that you ...
C: Genomic coordinates from GENCODE annotation file by Emily_Ensembl ♦ 16k
If you use the variation database rather than the gene database, you can add 1000 Genomes and/or ...
C: Bedtools intersect alternatives available by Friederike • 2.3k
If this is whole-genome sequencing, I recommend first running a basic intersect (either with bedt...
C: Bedtools intersect alternatives available by Alex Reynolds ♦ 26k
I don't know what overlap criteria that bedtools uses as a default, but `--element-of 1` is one o...

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