I have generated fastq files (R1& R2) from the mapped bam file and I am now interested in assembling those reads using velvet. I need guidance to how to run velveth, velvetg and viewing the output.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by Michael.Ante View PostHi Kaps,
you should have a look at the Bowtie2 homepage. There, it is explained in detail how the programs work. At the end of the manual is a "Lambda phage example", which has quite an overlap to your problem. It also has a SAMtools downstream section...
Cheers,
Michael
here is the feedback: samtools view -bS 4_S4_paired.sam 4_S4_paired.bam
[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
▒▒y▒▒
when with -bT, I get a similar feedback as;
samtools view -bT cp4genome.fa 4_S4_paired.sam 4_S4_paired.bam
[samfaipath] build FASTA index...
[fai_build_core] different line length in sequence '4_S4_contig_23'.
[samfaipath] fail to build FASTA index.
[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
where is the problem?
Comment
-
Hi Kaps,
tryCode:samtools view -S 4_S4_paired.sam | head
Code:samtools view -bSh 4_S4_paired.sam > 4_S4_paired.bam
Cheers,
Michael
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment