User: sullis02

gravatar for sullis02
sullis020
Reputation:
0
Status:
New User
Last seen:
3 months ago
Joined:
1 year, 4 months ago
Email:
s*******@nyu.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by sullis02

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
1.6k
views
1
answers
Comment: C: bedtools merge - removing features completly overlapped by other features
... Still fails: $ bedops -m out.bed | bedmap --echo-map --exact --skip-unmapped - out.bed | sort-bed - chr2 28 80 chr2 89 156 chr3 16 191 chr5 55 144 chr6 77 150 ...
written 10 months ago by sullis020
0
votes
1
answer
1.6k
views
1
answers
Comment: C: bedtools merge - removing features completly overlapped by other features
... And the awk script doesn't seem to be working either. (To be sure, I used the same A2.bed file as above). The awk script is executable. $ cat A2.bed chr1 80 101 id-0 chr1 100 120 id-1 chr1 110 112 id-2 chr1 114 117 id-3 chr1 12 ...
written 11 months ago by sullis020
0
votes
1
answer
1.6k
views
1
answers
Comment: C: bedtools merge - removing features completly overlapped by other features
... The bedops one-liner didn't work correctly with my input file (out.bed). Bedops version is 2.4.26 $ cat out.bed chr1 274 324 chr1 292 356 chr2 28 80 chr2 89 156 chr3 16 191 chr3 28 174 chr4 17 191 chr4 24 ...
written 11 months ago by sullis020
0
votes
4
answers
3.0k
views
4
answers
Comment: C: Misunderstood parameter of NCBI BLAST
... Which is actually properly cited in the Shah et al. paper: "This functionality was first reported as a bug to NCBI by Kumar (2015), and later documented in a blog post (Cock, 2015) by Peter Cock." ...
written 12 months ago by sullis020
0
votes
1
answer
494
views
1
answers
Comment: C: working with Sanger fasta + qual + clip files
... Oops, wrote to soon. Have you tried your script with input files that contain more than a single fasta/clip/qual record? With a single record as input (as in your example) it works fine. With normal fasta /qual/clip files (which contain numerous records) it doesn't work it reports ' clip id does ...
written 15 months ago by sullis020
0
votes
1
answer
494
views
1
answers
Comment: C: working with Sanger fasta + qual + clip files
... Thank you very much!! ...
written 15 months ago by sullis020
0
votes
1
answer
519
views
1
answers
Comment: C: adding pair info to fastq files, for BWA
... NB that even if bwa index chose the wrong -a option, bwa mem will still output a .sam file. So it's worth checking. ...
written 16 months ago by sullis020
0
votes
1
answer
519
views
1
answers
Comment: C: adding pair info to fastq files, for BWA
... Problem solved. It was due to incorrect bwa indexing. By default (I use v 0.7.17, though 0.7.15 exhibited the same behavior), the bwa index -a option is set to 'auto', which means bwa index itself decides whether to use the 'bwtsw' (large reference sequence) or 'is' (small) setting (or 'rb2' but I ...
written 16 months ago by sullis020
0
votes
1
answer
519
views
1
answers
Comment: C: adding pair info to fastq files, for BWA
... Sorry, my reply should have gone here. Instead it's following my first post up there. ...
written 16 months ago by sullis020
0
votes
1
answer
519
views
1
answers
Comment: A: adding pair info to fastq files, for BWA
... I also tried a completely different pair of fastq files, generated by our sequencing core (not downloaded), with headers like this R1.fastq @HWI-ST911:230:C4MVUACXX:2:1101:1483:2058 1:N:0:ACAGTG R2.fastq @HWI-ST911:230:C4MVUACXX:2:1101:1483:2058 2:N:0:ACAGTG run: [M::bw ...
written 16 months ago by sullis020

Latest awards to sullis02

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1490 users visited in the last hour