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Search: Posts Made By: madhavi
Forum: Bioinformatics 10-20-2016, 05:22 AM
Replies: 2
Views: 1,600
Posted By madhavi
Hello guys You both just change the command a...

Hello guys
You both just change the command a little bit and try the following command and check.And one more thing please place your reference trinity.fasta directly in the...
Forum: Introductions 08-11-2015, 12:37 AM
Replies: 0
Views: 612
Posted By madhavi
tbl2asn submission error

Hello all,
i am facing a problem while submitting transcripts.fas through tbl2asn.
according the guidelines i have created a template.sbt and nuclodtide.fas ,and downloaded tbl2asn.kept...
Forum: De novo discovery 03-23-2015, 03:04 AM
Replies: 5
Views: 2,354
Posted By madhavi
hi all oases is showing an error make: ***...

hi all
oases is showing an error make: *** [velvet] Error 2
help me to fix this thank u
Forum: Bioinformatics 03-12-2015, 01:04 AM
Replies: 4
Views: 1,631
Posted By madhavi
Hello oases make is not working out and giving...

Hello
oases make is not working out and giving error as rm -f obj/*.o obj/dbg/*.o
cd ../velvet && make -e obj
/bin/sh: 1: cd: can't cd to ../velvet
make: *** [velvet] Error 2?
thanks
Forum: Bioinformatics 03-11-2015, 12:07 AM
Replies: 6
Views: 3,144
Posted By madhavi
Hello mastal first of all thanks for ur reply. ...

Hello mastal
first of all thanks for ur reply.
i have tried this too but it is showing an error as 'compilation terminated.make: *** [obj/readSet.o] Error 1'
Forum: Bioinformatics 03-09-2015, 04:30 AM
Replies: 6
Views: 3,144
Posted By madhavi
Hii can anyone help me to run velvet with higher...

Hii can anyone help me to run velvet with higher hash value rather than 31 and also how to run velvet optimiser? (illumina short paied end reads)
thanks in advance
Forum: Complete Genomics 02-26-2015, 03:21 AM
Replies: 1
Views: 3,600
Posted By madhavi
hii everyone samtools showing an error when i...

hii everyone
samtools showing an error when i tried to create a bcf file
[bcf_sync] incorrect number of fields (0 != 5) at 0:0 [afs] 0:0.000
how to solve this? thank u
Forum: Illumina/Solexa 02-09-2015, 09:40 PM
Replies: 11
Views: 1,855
Posted By madhavi
Hii i am ruuning samtools to create variation...

Hii
i am ruuning samtools to create variation report by using the following commond it showed an error Segmentation fault (core dumped)
how to solve this ?
NGSprograms/samtools-1.2$ samtools...
Forum: Illumina/Solexa 02-06-2015, 01:03 AM
Replies: 11
Views: 1,855
Posted By madhavi
NGSprograms/bowtie2-2.2.4$ bowtie2 -p 12 -N 1 -t...

NGSprograms/bowtie2-2.2.4$ bowtie2 -p 12 -N 1 -t -x /NGSprograms/bowtie2_2.2.4/bt2-index/yeast_index -1 yeastR1.fastq, -2 yeastR2.fastq -S yeast.sam
Forum: Illumina/Solexa 02-06-2015, 12:45 AM
Replies: 11
Views: 1,855
Posted By madhavi
the command i used is bowtie2-2.2.4$ bowtie2 ...

the command i used is
bowtie2-2.2.4$ bowtie2 -p 12 -N 1 -t -x /bt2-index/yeast_index -1 testR1.fastq -2 testR2.fastq -S test.sam
Forum: Illumina/Solexa 02-05-2015, 11:40 PM
Replies: 11
Views: 1,855
Posted By madhavi
Hii dpryan Thanks i could successfully install...

Hii dpryan
Thanks i could successfully install and run bowtie2 to some extend. but after creating the reference index file and when i was trying to align reads it is showing an error like
Extra...
Forum: Illumina/Solexa 02-04-2015, 10:04 PM
Replies: 11
Views: 1,855
Posted By madhavi
Bowtie error

Hii
I tried to reinstall bowtie2, it is showing an error 'bin/sh: 1: clang++: not found
make: *** [bowtie2-build-s] Error 127'
help me to solve this thank u
Forum: Illumina/Solexa 01-30-2015, 10:05 PM
Replies: 11
Views: 1,855
Posted By madhavi
Fastq to Sam

Hii everyone i have read about conversion of Fastq to sam through picard tools and alignment with bowtie(which directly gives sam output) both dnt worked out with my fastq files ? please suggest any...
Forum: Bioinformatics 01-30-2015, 10:00 PM
Replies: 10
Views: 14,821
Posted By madhavi
Hi i am new to NGS analysis. I have read and...

Hi i am new to NGS analysis. I have read and tried many answers regarding converting fastq to sam through picard tools, But it dnt work out? is there any other way to do that?thank u.
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